Discussion:
http://www.bioperl.org/wiki/Bptutorial.pl
(too old to reply)
Jay Hannah
2006-05-31 13:07:10 UTC
Permalink
http://www.bioperl.org/wiki/Bptutorial.pl

I think I just partially fulfilled this TODO:

TODO: check if the POD is in the Wiki yet, and if not, put it here?

I used Pod::Simple::Wiki (format 'mediawiki') to burn bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the wiki page via my web browser. (Is that proper procedure? Is the plan to just do that manually from time to time as the document changes?)

Now what?

Should there be a new link on the far left of bioperl.org called "Tutorial"?

It's an amazing document. IMHO it should be listed prominently on bioperl.org.

HTH,

j
Brian Osborne
2006-05-31 13:58:01 UTC
Permalink
Jay,

Excellent! Now we need to answer a few more questions for ourselves:

- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.

- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.

- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.

Any thoughts on these?


Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the
wiki page via my web browser. (Is that proper procedure? Is the plan to just
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called "Tutorial"?
It's an amazing document. IMHO it should be listed prominently on bioperl.org.
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Bernd Web
2006-05-31 14:30:30 UTC
Permalink
Hi,

I am not sure to what extent bptutorial will be removed, but
I actually like having bptutorial.pl in my BioPerl base for reference.

regards,
Bernd
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the
wiki page via my web browser. (Is that proper procedure? Is the plan to just
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called "Tutorial"?
It's an amazing document. IMHO it should be listed prominently on bioperl.org.
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Jay Hannah
2006-06-01 01:54:01 UTC
Permalink
Post by Brian Osborne
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
We certainly wouldn't want to try to maintain two copies, one POD one in wiki. That would be the worst of all options. One option that hasn't been mentioned yet is to keep maintenance of that in POD in the distro (leaving the cool runability alone), and then flag that document as unchangeable in the wiki with a note on top "Maintenance of this document is done in POD in the distro. Submit POD patches to bioperl-l and we'll re-post an updated copy to this wiki."

Just a thought.
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
/README says this:

scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl

I'm personally not clear on the difference. Little stuff should start in examples/ and graduate to scripts/ once they've matured?

Is the doc/ tree being abandoned?

doc/faq (empty?)
doc/howto
doc/howto/examples
doc/howto/figs (empty?)
doc/howto/html (empty?)
doc/howto/pdf (empty?)
doc/howto/sgml (empty?)
doc/howto/txt (empty?)
doc/howto/xml (empty?)

Does all that stuff officially live in and is being changed in the wiki, never to return to the distro?

Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts didn't convert well. I've never done that conversion before, and know nothing about mediawiki. I just blindly let Pod::Simple::Wiki do its thing then ran off to work. :)
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a master "documentation" page linked on the left cascading like so?

Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials

(What's the conceptual difference between a HOWTO and a tutorial?)

It's hard for me to dive into a wiki lifestyle for the huge documentation pillars since it can't ever get back into the distro... (can it?) Small, throw away stuff is great for the wiki, but huge, established, thoughtful, long documents should be left in the distro? Present (and searchable) on the wiki but static?

Why isn't the short "Current events" just listed on the top of the "News" page?

Sick of my endless questions yet? -grin-

j
Mauricio Herrera Cuadra
2006-06-01 16:36:07 UTC
Permalink
Post by Jay Hannah
Post by Mauricio Herrera Cuadra
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
Nice idea, I'll check with Jason if it's possible (in mediawiki) to
create a new Documentation sidebar to hold this 4 sections.
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
My concept is that Tutorials cover a wider aspect of BioPerl, contrary
to the HOWTO's which focus on a certain topic.
Post by Jay Hannah
Why isn't the short "Current events" just listed on the top of the "News" page?
I don't know, maybe because it was important when Jason started the Wiki
a couple of months ago. Do you think it should be erased from the sidebar?
Post by Jay Hannah
Sick of my endless questions yet? -grin-
j
Of course not! :)

Mauricio.
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-06-01 16:36:07 UTC
Permalink
Post by Jay Hannah
Post by Mauricio Herrera Cuadra
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
Nice idea, I'll check with Jason if it's possible (in mediawiki) to
create a new Documentation sidebar to hold this 4 sections.
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
My concept is that Tutorials cover a wider aspect of BioPerl, contrary
to the HOWTO's which focus on a certain topic.
Post by Jay Hannah
Why isn't the short "Current events" just listed on the top of the "News" page?
I don't know, maybe because it was important when Jason started the Wiki
a couple of months ago. Do you think it should be erased from the sidebar?
Post by Jay Hannah
Sick of my endless questions yet? -grin-
j
Of course not! :)

Mauricio.
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-06-01 16:36:07 UTC
Permalink
Post by Jay Hannah
Post by Mauricio Herrera Cuadra
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
Nice idea, I'll check with Jason if it's possible (in mediawiki) to
create a new Documentation sidebar to hold this 4 sections.
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
My concept is that Tutorials cover a wider aspect of BioPerl, contrary
to the HOWTO's which focus on a certain topic.
Post by Jay Hannah
Why isn't the short "Current events" just listed on the top of the "News" page?
I don't know, maybe because it was important when Jason started the Wiki
a couple of months ago. Do you think it should be erased from the sidebar?
Post by Jay Hannah
Sick of my endless questions yet? -grin-
j
Of course not! :)

Mauricio.
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-06-01 16:36:07 UTC
Permalink
Post by Jay Hannah
Post by Mauricio Herrera Cuadra
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
Nice idea, I'll check with Jason if it's possible (in mediawiki) to
create a new Documentation sidebar to hold this 4 sections.
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
My concept is that Tutorials cover a wider aspect of BioPerl, contrary
to the HOWTO's which focus on a certain topic.
Post by Jay Hannah
Why isn't the short "Current events" just listed on the top of the "News" page?
I don't know, maybe because it was important when Jason started the Wiki
a couple of months ago. Do you think it should be erased from the sidebar?
Post by Jay Hannah
Sick of my endless questions yet? -grin-
j
Of course not! :)

Mauricio.
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Bernd Web
2006-05-31 14:30:30 UTC
Permalink
Hi,

I am not sure to what extent bptutorial will be removed, but
I actually like having bptutorial.pl in my BioPerl base for reference.

regards,
Bernd
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the
wiki page via my web browser. (Is that proper procedure? Is the plan to just
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called "Tutorial"?
It's an amazing document. IMHO it should be listed prominently on bioperl.org.
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Jay Hannah
2006-06-01 01:54:01 UTC
Permalink
Post by Brian Osborne
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
We certainly wouldn't want to try to maintain two copies, one POD one in wiki. That would be the worst of all options. One option that hasn't been mentioned yet is to keep maintenance of that in POD in the distro (leaving the cool runability alone), and then flag that document as unchangeable in the wiki with a note on top "Maintenance of this document is done in POD in the distro. Submit POD patches to bioperl-l and we'll re-post an updated copy to this wiki."

Just a thought.
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
/README says this:

scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl

I'm personally not clear on the difference. Little stuff should start in examples/ and graduate to scripts/ once they've matured?

Is the doc/ tree being abandoned?

doc/faq (empty?)
doc/howto
doc/howto/examples
doc/howto/figs (empty?)
doc/howto/html (empty?)
doc/howto/pdf (empty?)
doc/howto/sgml (empty?)
doc/howto/txt (empty?)
doc/howto/xml (empty?)

Does all that stuff officially live in and is being changed in the wiki, never to return to the distro?

Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts didn't convert well. I've never done that conversion before, and know nothing about mediawiki. I just blindly let Pod::Simple::Wiki do its thing then ran off to work. :)
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a master "documentation" page linked on the left cascading like so?

Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials

(What's the conceptual difference between a HOWTO and a tutorial?)

It's hard for me to dive into a wiki lifestyle for the huge documentation pillars since it can't ever get back into the distro... (can it?) Small, throw away stuff is great for the wiki, but huge, established, thoughtful, long documents should be left in the distro? Present (and searchable) on the wiki but static?

Why isn't the short "Current events" just listed on the top of the "News" page?

Sick of my endless questions yet? -grin-

j
Bernd Web
2006-05-31 14:30:30 UTC
Permalink
Hi,

I am not sure to what extent bptutorial will be removed, but
I actually like having bptutorial.pl in my BioPerl base for reference.

regards,
Bernd
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the
wiki page via my web browser. (Is that proper procedure? Is the plan to just
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called "Tutorial"?
It's an amazing document. IMHO it should be listed prominently on bioperl.org.
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Jay Hannah
2006-06-01 01:54:01 UTC
Permalink
Post by Brian Osborne
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
We certainly wouldn't want to try to maintain two copies, one POD one in wiki. That would be the worst of all options. One option that hasn't been mentioned yet is to keep maintenance of that in POD in the distro (leaving the cool runability alone), and then flag that document as unchangeable in the wiki with a note on top "Maintenance of this document is done in POD in the distro. Submit POD patches to bioperl-l and we'll re-post an updated copy to this wiki."

Just a thought.
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
/README says this:

scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl

I'm personally not clear on the difference. Little stuff should start in examples/ and graduate to scripts/ once they've matured?

Is the doc/ tree being abandoned?

doc/faq (empty?)
doc/howto
doc/howto/examples
doc/howto/figs (empty?)
doc/howto/html (empty?)
doc/howto/pdf (empty?)
doc/howto/sgml (empty?)
doc/howto/txt (empty?)
doc/howto/xml (empty?)

Does all that stuff officially live in and is being changed in the wiki, never to return to the distro?

Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts didn't convert well. I've never done that conversion before, and know nothing about mediawiki. I just blindly let Pod::Simple::Wiki do its thing then ran off to work. :)
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a master "documentation" page linked on the left cascading like so?

Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials

(What's the conceptual difference between a HOWTO and a tutorial?)

It's hard for me to dive into a wiki lifestyle for the huge documentation pillars since it can't ever get back into the distro... (can it?) Small, throw away stuff is great for the wiki, but huge, established, thoughtful, long documents should be left in the distro? Present (and searchable) on the wiki but static?

Why isn't the short "Current events" just listed on the top of the "News" page?

Sick of my endless questions yet? -grin-

j
Bernd Web
2006-05-31 14:30:30 UTC
Permalink
Hi,

I am not sure to what extent bptutorial will be removed, but
I actually like having bptutorial.pl in my BioPerl base for reference.

regards,
Bernd
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the
wiki page via my web browser. (Is that proper procedure? Is the plan to just
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called "Tutorial"?
It's an amazing document. IMHO it should be listed prominently on bioperl.org.
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Phillip SanMiguel
2006-06-24 14:17:46 UTC
Permalink
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
available to any given object. Eg:

bptutorial.pl 100 Bio::PrimarySeq

***Methods for Object Bio::PrimarySeq ********


Methods taken from package Bio::IdentifiableI
lsid_string namespace_string

Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version

Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc

Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose

Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented


Phillip SanMiguel
Mauricio Herrera Cuadra
2006-06-24 15:27:03 UTC
Permalink
Hi Philip,

Have you tried the Deobfuscator interface? It's a newer and better way
to browse all the methods available in BioPerl:

http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi

Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Phillip SanMiguel
2006-06-24 16:59:21 UTC
Permalink
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better way
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Mauricio Herrera Cuadra
2006-06-24 17:35:54 UTC
Permalink
Currently I'm modifying the Deobfuscator so it'd be capable of browsing
the different BioPerl packages as well as their respective releases, but
haven't got many spare time to finish it :(

Dave and I committed the Deobfuscator into the bioperl-live source tree
(in /doc directory), so it'd be included in future releases of BioPerl.
I'm also working on a command line version which won't need a CGI
environment to have the same functionality, this would address the web
access situation that you mention.
Post by Phillip SanMiguel
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better way
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Phillip SanMiguel
2006-06-24 17:48:15 UTC
Permalink
Yes, that would be better than bptutorial.pl 100 then. For some modules
bptutorial.pl 100 doesn't seem to give any of the methods they have
access to. Whereas the deobfuscator does.
Post by Mauricio Herrera Cuadra
Currently I'm modifying the Deobfuscator so it'd be capable of
browsing the different BioPerl packages as well as their respective
releases, but haven't got many spare time to finish it :(
Dave and I committed the Deobfuscator into the bioperl-live source
tree (in /doc directory), so it'd be included in future releases of
BioPerl. I'm also working on a command line version which won't need a
CGI environment to have the same functionality, this would address the
web access situation that you mention.
Post by Phillip SanMiguel
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of
bptutorial.pl--this was described in Tisdall's _Mastering Perl for
Bioinformatics_. It is the only purpose I've ever used
bptutorial.pl for--to find all the methods available to any given
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority
can_call_new desc
description direct_seq_set display_id display_name id
is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-24 19:07:06 UTC
Permalink
As a quickie method I use the script from the FAQ; you have to
install Class::Inspector:

#!/usr/bin/perl -w
use Class::Inspector;
$class = shift || die "Usage: methods perl_class_name\n";
eval "require $class";
print join ("\n", sort @{Class::Inspector->methods
($class,'full','public')}), "\n";

Works well, though doesn't have the links and so on like
Deobfuscator; I use HTML-generated ActiveState docs:

glaciers-115 chris$ methods.pl Bio::SeqIO
Bio::Root::IO::catfile
Bio::Root::IO::close
Bio::Root::IO::dup
Bio::Root::IO::exists_exe
Bio::Root::IO::file
Bio::Root::IO::flush
Bio::Root::IO::gensym
Bio::Root::IO::mode
Bio::Root::IO::noclose
Bio::Root::IO::qualify
Bio::Root::IO::qualify_to_ref
Bio::Root::IO::rmtree
Bio::Root::IO::tempdir
Bio::Root::IO::tempfile
Bio::Root::IO::ungensym
Bio::Root::Root::debug
Bio::Root::Root::except
Bio::Root::Root::finally
Bio::Root::Root::otherwise
Bio::Root::Root::throw
Bio::Root::Root::try
Bio::Root::Root::verbose
Bio::Root::Root::with
Bio::Root::RootI::carp
Bio::Root::RootI::confess
Bio::Root::RootI::deprecated
Bio::Root::RootI::stack_trace
Bio::Root::RootI::stack_trace_dump
Bio::Root::RootI::throw_not_implemented
Bio::Root::RootI::warn
Bio::Root::RootI::warn_not_implemented
Bio::SeqIO::DESTROY
Bio::SeqIO::PRINT
Bio::SeqIO::READLINE
Bio::SeqIO::TIEHANDLE
Bio::SeqIO::alphabet
Bio::SeqIO::fh
Bio::SeqIO::location_factory
Bio::SeqIO::new
Bio::SeqIO::newFh
Bio::SeqIO::next_seq
Bio::SeqIO::object_factory
Bio::SeqIO::sequence_builder
Bio::SeqIO::sequence_factory
Bio::SeqIO::write_seq


Chris
Post by Phillip SanMiguel
Yes, that would be better than bptutorial.pl 100 then. For some modules
bptutorial.pl 100 doesn't seem to give any of the methods they have
access to. Whereas the deobfuscator does.
Post by Mauricio Herrera Cuadra
Currently I'm modifying the Deobfuscator so it'd be capable of
browsing the different BioPerl packages as well as their respective
releases, but haven't got many spare time to finish it :(
Dave and I committed the Deobfuscator into the bioperl-live source
tree (in /doc directory), so it'd be included in future releases of
BioPerl. I'm also working on a command line version which won't need a
CGI environment to have the same functionality, this would address the
web access situation that you mention.
Post by Phillip SanMiguel
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
Excellent! Now we need to answer a few more questions for
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of
bptutorial.pl--this was described in Tisdall's _Mastering Perl for
Bioinformatics_. It is the only purpose I've ever used
bptutorial.pl for--to find all the methods available to any given
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority
can_call_new desc
description direct_seq_set display_id display_name id
is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
Chris Fields
2006-06-24 19:07:06 UTC
Permalink
As a quickie method I use the script from the FAQ; you have to
install Class::Inspector:

#!/usr/bin/perl -w
use Class::Inspector;
$class = shift || die "Usage: methods perl_class_name\n";
eval "require $class";
print join ("\n", sort @{Class::Inspector->methods
($class,'full','public')}), "\n";

Works well, though doesn't have the links and so on like
Deobfuscator; I use HTML-generated ActiveState docs:

glaciers-115 chris$ methods.pl Bio::SeqIO
Bio::Root::IO::catfile
Bio::Root::IO::close
Bio::Root::IO::dup
Bio::Root::IO::exists_exe
Bio::Root::IO::file
Bio::Root::IO::flush
Bio::Root::IO::gensym
Bio::Root::IO::mode
Bio::Root::IO::noclose
Bio::Root::IO::qualify
Bio::Root::IO::qualify_to_ref
Bio::Root::IO::rmtree
Bio::Root::IO::tempdir
Bio::Root::IO::tempfile
Bio::Root::IO::ungensym
Bio::Root::Root::debug
Bio::Root::Root::except
Bio::Root::Root::finally
Bio::Root::Root::otherwise
Bio::Root::Root::throw
Bio::Root::Root::try
Bio::Root::Root::verbose
Bio::Root::Root::with
Bio::Root::RootI::carp
Bio::Root::RootI::confess
Bio::Root::RootI::deprecated
Bio::Root::RootI::stack_trace
Bio::Root::RootI::stack_trace_dump
Bio::Root::RootI::throw_not_implemented
Bio::Root::RootI::warn
Bio::Root::RootI::warn_not_implemented
Bio::SeqIO::DESTROY
Bio::SeqIO::PRINT
Bio::SeqIO::READLINE
Bio::SeqIO::TIEHANDLE
Bio::SeqIO::alphabet
Bio::SeqIO::fh
Bio::SeqIO::location_factory
Bio::SeqIO::new
Bio::SeqIO::newFh
Bio::SeqIO::next_seq
Bio::SeqIO::object_factory
Bio::SeqIO::sequence_builder
Bio::SeqIO::sequence_factory
Bio::SeqIO::write_seq


Chris
Post by Phillip SanMiguel
Yes, that would be better than bptutorial.pl 100 then. For some modules
bptutorial.pl 100 doesn't seem to give any of the methods they have
access to. Whereas the deobfuscator does.
Post by Mauricio Herrera Cuadra
Currently I'm modifying the Deobfuscator so it'd be capable of
browsing the different BioPerl packages as well as their respective
releases, but haven't got many spare time to finish it :(
Dave and I committed the Deobfuscator into the bioperl-live source
tree (in /doc directory), so it'd be included in future releases of
BioPerl. I'm also working on a command line version which won't need a
CGI environment to have the same functionality, this would address the
web access situation that you mention.
Post by Phillip SanMiguel
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
Excellent! Now we need to answer a few more questions for
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of
bptutorial.pl--this was described in Tisdall's _Mastering Perl for
Bioinformatics_. It is the only purpose I've ever used
bptutorial.pl for--to find all the methods available to any given
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority
can_call_new desc
description direct_seq_set display_id display_name id
is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
Chris Fields
2006-06-24 19:07:06 UTC
Permalink
As a quickie method I use the script from the FAQ; you have to
install Class::Inspector:

#!/usr/bin/perl -w
use Class::Inspector;
$class = shift || die "Usage: methods perl_class_name\n";
eval "require $class";
print join ("\n", sort @{Class::Inspector->methods
($class,'full','public')}), "\n";

Works well, though doesn't have the links and so on like
Deobfuscator; I use HTML-generated ActiveState docs:

glaciers-115 chris$ methods.pl Bio::SeqIO
Bio::Root::IO::catfile
Bio::Root::IO::close
Bio::Root::IO::dup
Bio::Root::IO::exists_exe
Bio::Root::IO::file
Bio::Root::IO::flush
Bio::Root::IO::gensym
Bio::Root::IO::mode
Bio::Root::IO::noclose
Bio::Root::IO::qualify
Bio::Root::IO::qualify_to_ref
Bio::Root::IO::rmtree
Bio::Root::IO::tempdir
Bio::Root::IO::tempfile
Bio::Root::IO::ungensym
Bio::Root::Root::debug
Bio::Root::Root::except
Bio::Root::Root::finally
Bio::Root::Root::otherwise
Bio::Root::Root::throw
Bio::Root::Root::try
Bio::Root::Root::verbose
Bio::Root::Root::with
Bio::Root::RootI::carp
Bio::Root::RootI::confess
Bio::Root::RootI::deprecated
Bio::Root::RootI::stack_trace
Bio::Root::RootI::stack_trace_dump
Bio::Root::RootI::throw_not_implemented
Bio::Root::RootI::warn
Bio::Root::RootI::warn_not_implemented
Bio::SeqIO::DESTROY
Bio::SeqIO::PRINT
Bio::SeqIO::READLINE
Bio::SeqIO::TIEHANDLE
Bio::SeqIO::alphabet
Bio::SeqIO::fh
Bio::SeqIO::location_factory
Bio::SeqIO::new
Bio::SeqIO::newFh
Bio::SeqIO::next_seq
Bio::SeqIO::object_factory
Bio::SeqIO::sequence_builder
Bio::SeqIO::sequence_factory
Bio::SeqIO::write_seq


Chris
Post by Phillip SanMiguel
Yes, that would be better than bptutorial.pl 100 then. For some modules
bptutorial.pl 100 doesn't seem to give any of the methods they have
access to. Whereas the deobfuscator does.
Post by Mauricio Herrera Cuadra
Currently I'm modifying the Deobfuscator so it'd be capable of
browsing the different BioPerl packages as well as their respective
releases, but haven't got many spare time to finish it :(
Dave and I committed the Deobfuscator into the bioperl-live source
tree (in /doc directory), so it'd be included in future releases of
BioPerl. I'm also working on a command line version which won't need a
CGI environment to have the same functionality, this would address the
web access situation that you mention.
Post by Phillip SanMiguel
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
Excellent! Now we need to answer a few more questions for
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of
bptutorial.pl--this was described in Tisdall's _Mastering Perl for
Bioinformatics_. It is the only purpose I've ever used
bptutorial.pl for--to find all the methods available to any given
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority
can_call_new desc
description direct_seq_set display_id display_name id
is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
Phillip SanMiguel
2006-06-24 17:48:15 UTC
Permalink
Yes, that would be better than bptutorial.pl 100 then. For some modules
bptutorial.pl 100 doesn't seem to give any of the methods they have
access to. Whereas the deobfuscator does.
Post by Mauricio Herrera Cuadra
Currently I'm modifying the Deobfuscator so it'd be capable of
browsing the different BioPerl packages as well as their respective
releases, but haven't got many spare time to finish it :(
Dave and I committed the Deobfuscator into the bioperl-live source
tree (in /doc directory), so it'd be included in future releases of
BioPerl. I'm also working on a command line version which won't need a
CGI environment to have the same functionality, this would address the
web access situation that you mention.
Post by Phillip SanMiguel
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of
bptutorial.pl--this was described in Tisdall's _Mastering Perl for
Bioinformatics_. It is the only purpose I've ever used
bptutorial.pl for--to find all the methods available to any given
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority
can_call_new desc
description direct_seq_set display_id display_name id
is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Phillip SanMiguel
2006-06-24 17:48:15 UTC
Permalink
Yes, that would be better than bptutorial.pl 100 then. For some modules
bptutorial.pl 100 doesn't seem to give any of the methods they have
access to. Whereas the deobfuscator does.
Post by Mauricio Herrera Cuadra
Currently I'm modifying the Deobfuscator so it'd be capable of
browsing the different BioPerl packages as well as their respective
releases, but haven't got many spare time to finish it :(
Dave and I committed the Deobfuscator into the bioperl-live source
tree (in /doc directory), so it'd be included in future releases of
BioPerl. I'm also working on a command line version which won't need a
CGI environment to have the same functionality, this would address the
web access situation that you mention.
Post by Phillip SanMiguel
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of
bptutorial.pl--this was described in Tisdall's _Mastering Perl for
Bioinformatics_. It is the only purpose I've ever used
bptutorial.pl for--to find all the methods available to any given
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority
can_call_new desc
description direct_seq_set display_id display_name id
is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Mauricio Herrera Cuadra
2006-06-24 17:35:54 UTC
Permalink
Currently I'm modifying the Deobfuscator so it'd be capable of browsing
the different BioPerl packages as well as their respective releases, but
haven't got many spare time to finish it :(

Dave and I committed the Deobfuscator into the bioperl-live source tree
(in /doc directory), so it'd be included in future releases of BioPerl.
I'm also working on a command line version which won't need a CGI
environment to have the same functionality, this would address the web
access situation that you mention.
Post by Phillip SanMiguel
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better way
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-06-24 17:35:54 UTC
Permalink
Currently I'm modifying the Deobfuscator so it'd be capable of browsing
the different BioPerl packages as well as their respective releases, but
haven't got many spare time to finish it :(

Dave and I committed the Deobfuscator into the bioperl-live source tree
(in /doc directory), so it'd be included in future releases of BioPerl.
I'm also working on a command line version which won't need a CGI
environment to have the same functionality, this would address the web
access situation that you mention.
Post by Phillip SanMiguel
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better way
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Phillip SanMiguel
2006-06-24 16:59:21 UTC
Permalink
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better way
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Phillip SanMiguel
2006-06-24 16:59:21 UTC
Permalink
Yes I have. It is very useful.
But in situations where I don't have web access? Or I am working with
Bioperl 1.5?
Post by Mauricio Herrera Cuadra
Hi Philip,
Have you tried the Deobfuscator interface? It's a newer and better way
http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi
Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Mauricio Herrera Cuadra
2006-06-24 15:27:03 UTC
Permalink
Hi Philip,

Have you tried the Deobfuscator interface? It's a newer and better way
to browse all the methods available in BioPerl:

http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi

Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-06-24 15:27:03 UTC
Permalink
Hi Philip,

Have you tried the Deobfuscator interface? It's a newer and better way
to browse all the methods available in BioPerl:

http://bioperl.org/wiki/Deobfuscator
http://bioperl.org/cgi-bin/deob_interface.cgi

Regards,
Mauricio.
Post by Phillip SanMiguel
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
bptutorial.pl 100 Bio::PrimarySeq
***Methods for Object Bio::PrimarySeq ********
Methods taken from package Bio::IdentifiableI
lsid_string namespace_string
Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version
Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc
Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose
Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented
Phillip SanMiguel
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Phillip SanMiguel
2006-06-24 14:17:46 UTC
Permalink
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
available to any given object. Eg:

bptutorial.pl 100 Bio::PrimarySeq

***Methods for Object Bio::PrimarySeq ********


Methods taken from package Bio::IdentifiableI
lsid_string namespace_string

Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version

Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc

Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose

Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented


Phillip SanMiguel
Phillip SanMiguel
2006-06-24 14:17:46 UTC
Permalink
Post by Brian Osborne
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
I would be very disappointed to lose one part of bptutorial.pl--this was
described in Tisdall's _Mastering Perl for Bioinformatics_. It is the
only purpose I've ever used bptutorial.pl for--to find all the methods
available to any given object. Eg:

bptutorial.pl 100 Bio::PrimarySeq

***Methods for Object Bio::PrimarySeq ********


Methods taken from package Bio::IdentifiableI
lsid_string namespace_string

Methods taken from package Bio::PrimarySeq
accession accession_number alphabet authority can_call_new desc
description direct_seq_set display_id display_name id is_circular
length namespace new object_id primary_id seq
subseq validate_seq version

Methods taken from package Bio::PrimarySeqI
moltype revcom translate trunc

Methods taken from package Bio::Root::Root
DESTROY confess debug throw verbose

Methods taken from package Bio::Root::RootI
carp deprecated stack_trace stack_trace_dump
throw_not_implemented warn
warn_not_implemented


Phillip SanMiguel
Jay Hannah
2006-06-01 01:54:01 UTC
Permalink
Post by Brian Osborne
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
We certainly wouldn't want to try to maintain two copies, one POD one in wiki. That would be the worst of all options. One option that hasn't been mentioned yet is to keep maintenance of that in POD in the distro (leaving the cool runability alone), and then flag that document as unchangeable in the wiki with a note on top "Maintenance of this document is done in POD in the distro. Submit POD patches to bioperl-l and we'll re-post an updated copy to this wiki."

Just a thought.
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
/README says this:

scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl

I'm personally not clear on the difference. Little stuff should start in examples/ and graduate to scripts/ once they've matured?

Is the doc/ tree being abandoned?

doc/faq (empty?)
doc/howto
doc/howto/examples
doc/howto/figs (empty?)
doc/howto/html (empty?)
doc/howto/pdf (empty?)
doc/howto/sgml (empty?)
doc/howto/txt (empty?)
doc/howto/xml (empty?)

Does all that stuff officially live in and is being changed in the wiki, never to return to the distro?

Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts didn't convert well. I've never done that conversion before, and know nothing about mediawiki. I just blindly let Pod::Simple::Wiki do its thing then ran off to work. :)
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a master "documentation" page linked on the left cascading like so?

Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials

(What's the conceptual difference between a HOWTO and a tutorial?)

It's hard for me to dive into a wiki lifestyle for the huge documentation pillars since it can't ever get back into the distro... (can it?) Small, throw away stuff is great for the wiki, but huge, established, thoughtful, long documents should be left in the distro? Present (and searchable) on the wiki but static?

Why isn't the short "Current events" just listed on the top of the "News" page?

Sick of my endless questions yet? -grin-

j
Chris Fields
2006-05-31 16:34:54 UTC
Permalink
Brian, Jay,

I think it would be nice to have the tutorial prominently displayed somehow
(Jay's suggestion), with a link provided via the tutorials page. Hopefully
this will help with the bioperl newbies.

Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!

Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes,
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could
be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan to
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Mauricio Herrera Cuadra
2006-05-31 22:49:03 UTC
Permalink
Brian, Jay, Chris,

I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.

I don't think it should be a lot of problem to maintain both tutorials,
as long as the 'main' one is the one in the CVS tree. By reading what
Jay did in order to convert it into mediawiki format, I suppose this can
be easily done again for each new change to the script (again, this is
just my guessing). Besides, as far as I've seen, there aren't frequent
commits to the script at all.

I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.

Regards,
Mauricio.
Post by Chris Fields
Brian, Jay,
I think it would be nice to have the tutorial prominently displayed somehow
(Jay's suggestion), with a link provided via the tutorials page. Hopefully
this will help with the bioperl newbies.
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes,
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could
be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan to
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-05-31 22:49:03 UTC
Permalink
Brian, Jay, Chris,

I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.

I don't think it should be a lot of problem to maintain both tutorials,
as long as the 'main' one is the one in the CVS tree. By reading what
Jay did in order to convert it into mediawiki format, I suppose this can
be easily done again for each new change to the script (again, this is
just my guessing). Besides, as far as I've seen, there aren't frequent
commits to the script at all.

I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.

Regards,
Mauricio.
Post by Chris Fields
Brian, Jay,
I think it would be nice to have the tutorial prominently displayed somehow
(Jay's suggestion), with a link provided via the tutorials page. Hopefully
this will help with the bioperl newbies.
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes,
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could
be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan to
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-05-31 22:49:03 UTC
Permalink
Brian, Jay, Chris,

I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.

I don't think it should be a lot of problem to maintain both tutorials,
as long as the 'main' one is the one in the CVS tree. By reading what
Jay did in order to convert it into mediawiki format, I suppose this can
be easily done again for each new change to the script (again, this is
just my guessing). Besides, as far as I've seen, there aren't frequent
commits to the script at all.

I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.

Regards,
Mauricio.
Post by Chris Fields
Brian, Jay,
I think it would be nice to have the tutorial prominently displayed somehow
(Jay's suggestion), with a link provided via the tutorials page. Hopefully
this will help with the bioperl newbies.
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes,
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could
be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan to
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-05-31 22:49:03 UTC
Permalink
Brian, Jay, Chris,

I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.

I don't think it should be a lot of problem to maintain both tutorials,
as long as the 'main' one is the one in the CVS tree. By reading what
Jay did in order to convert it into mediawiki format, I suppose this can
be easily done again for each new change to the script (again, this is
just my guessing). Besides, as far as I've seen, there aren't frequent
commits to the script at all.

I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.

Regards,
Mauricio.
Post by Chris Fields
Brian, Jay,
I think it would be nice to have the tutorial prominently displayed somehow
(Jay's suggestion), with a link provided via the tutorials page. Hopefully
this will help with the bioperl newbies.
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes,
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could
be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan to
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Chris Fields
2006-06-01 00:56:12 UTC
Permalink
Mauricio et al,

Sounds good, except that there are a few issues with the formatting done by
Pod::Simple::Wiki, such as changing some things to <code> tags when they
obviously aren't code; I don't know if thee is a work around for that
(Jay?). It may not be anything too serious though.

There was a similar issue with the INSTALL doc conversion to wiki that I ran
into, in that I don't think it will be easy converting one way or the other
(POD->wiki or wiki->POD or text), so syncing updates with wiki and CVS docs
could be an issue we'll have to face in the future.

We could strip the POD out of the script and have the docs on the wiki
(Brian's idea), or have minimal POD in the tutorial and keep the wiki
updated, just to simplify things, but this may not appeal to those who use
perldoc frequently (I personally use browsable prettified HTML).

cjf
-----Original Message-----
From: Mauricio Herrera Cuadra [mailto:arareko at campus.iztacala.unam.mx]
Sent: Wednesday, May 31, 2006 5:49 PM
To: Chris Fields
Cc: 'Brian Osborne'; 'Jay Hannah'; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Brian, Jay, Chris,
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
I don't think it should be a lot of problem to maintain both tutorials,
as long as the 'main' one is the one in the CVS tree. By reading what
Jay did in order to convert it into mediawiki format, I suppose this can
be easily done again for each new change to the script (again, this is
just my guessing). Besides, as far as I've seen, there aren't frequent
commits to the script at all.
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Regards,
Mauricio.
Post by Chris Fields
Brian, Jay,
I think it would be nice to have the tutorial prominently displayed
somehow
Post by Chris Fields
(Jay's suggestion), with a link provided via the tutorials page.
Hopefully
Post by Chris Fields
this will help with the bioperl newbies.
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or
more
Post by Chris Fields
spaces preceding a line denotes code for some reason). Not much you can
do
Post by Chris Fields
in these cases except remove the extra spaces in those spots. Looking
good
Post by Chris Fields
though!
Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say
yes,
Post by Chris Fields
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly
could
Post by Chris Fields
be
excised and put into the examples/ directory, for example, but this
would
Post by Chris Fields
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan
to
Post by Chris Fields
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Brian Osborne
2006-06-01 01:37:15 UTC
Permalink
Mauricio,

Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that the
documentation is more important than the script, and this is what my last
letter was asking, in part: is the script important? Or can we focus on the
text/POD part?

Brian O.


On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
Mauricio Herrera Cuadra
2006-06-01 16:13:05 UTC
Permalink
You're right Brian. I also think that the text/POD part is more
important than the script. Since we're more into moving everything to
the Wiki, I believe this would be the right approach.

Moving the script part of the tutorial into the examples/ directory is
also a nice idea.

Mauricio.
Post by Brian Osborne
Mauricio,
Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that the
documentation is more important than the script, and this is what my last
letter was asking, in part: is the script important? Or can we focus on the
text/POD part?
Brian O.
On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-06-01 16:13:05 UTC
Permalink
You're right Brian. I also think that the text/POD part is more
important than the script. Since we're more into moving everything to
the Wiki, I believe this would be the right approach.

Moving the script part of the tutorial into the examples/ directory is
also a nice idea.

Mauricio.
Post by Brian Osborne
Mauricio,
Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that the
documentation is more important than the script, and this is what my last
letter was asking, in part: is the script important? Or can we focus on the
text/POD part?
Brian O.
On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-06-01 16:13:05 UTC
Permalink
You're right Brian. I also think that the text/POD part is more
important than the script. Since we're more into moving everything to
the Wiki, I believe this would be the right approach.

Moving the script part of the tutorial into the examples/ directory is
also a nice idea.

Mauricio.
Post by Brian Osborne
Mauricio,
Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that the
documentation is more important than the script, and this is what my last
letter was asking, in part: is the script important? Or can we focus on the
text/POD part?
Brian O.
On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Mauricio Herrera Cuadra
2006-06-01 16:13:05 UTC
Permalink
You're right Brian. I also think that the text/POD part is more
important than the script. Since we're more into moving everything to
the Wiki, I believe this would be the right approach.

Moving the script part of the tutorial into the examples/ directory is
also a nice idea.

Mauricio.
Post by Brian Osborne
Mauricio,
Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that the
documentation is more important than the script, and this is what my last
letter was asking, in part: is the script important? Or can we focus on the
text/POD part?
Brian O.
On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Chris Fields
2006-06-01 03:09:38 UTC
Permalink
...
Post by Jay Hannah
We certainly wouldn't want to try to maintain two copies, one POD one in
wiki. That would be the worst of all options. One option that hasn't been
mentioned yet is to keep maintenance of that in POD in the distro (leaving
the cool runability alone), and then flag that document as unchangeable in
the wiki with a note on top "Maintenance of this document is done in POD
in the distro. Submit POD patches to bioperl-l and we'll re-post an
updated copy to this wiki."
Just a thought.
There are probably three schools of thought on docs: those that like nice
docs with links within and beyond BioPerl (hence the wiki), those who like
including docs with the distribution, and those that would like both. The
latter would be nice but isn't realistic unless we can come up with a way to
sync changes between the wiki and CVS those docs we want to include with the
distribution w/o too much trouble. I'm in the first school of thought since
rich text with links is better and more informative than plain text any day.
It might be a very small school though...
Post by Jay Hannah
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly
could be
Post by Brian Osborne
excised and put into the examples/ directory, for example, but this
would
Post by Brian Osborne
break a few of the paths that are being used.
scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl
I'm personally not clear on the difference. Little stuff should start in
examples/ and graduate to scripts/ once they've matured?
Is the doc/ tree being abandoned?
Most docs have been moved over to the wiki, which generates nicely formatted
docs for printing.
...
Post by Jay Hannah
Does all that stuff officially live in and is being changed in the wiki,
never to return to the distro?
It's easier to add changes in the wiki and add markup, links, etc. Much
richer text, so on.
Post by Jay Hannah
Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or
more
Post by Brian Osborne
spaces preceding a line denotes code for some reason). Not much you can
do
Post by Brian Osborne
in these cases except remove the extra spaces in those spots. Looking
good
Post by Brian Osborne
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts
didn't convert well. I've never done that conversion before, and know
nothing about mediawiki. I just blindly let Pod::Simple::Wiki do its thing
then ran off to work. :)
No big deal.
Post by Jay Hannah
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a
master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
Okay, though Mauricio may know a bit more on how/if this can be done.
Mauricio?
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
I believe the reasoning is along these lines: HOWTO's are focused in on
specific areas (graphics, trees, BLAST report parsing, etc) and thus usually
has greater detail. The tutorials are more broadly based (sort of a general
bioperl HOWTO). The only exception is the Beginner's HOWTO, but even that
has additional information over the tutorial (at least it did the last time
I looked at the tutorial, which has been a while).
Post by Jay Hannah
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on
the wiki but static?
Hence the problem we face now. It is something we need to really look into
before adding too much more to the wiki. IMHO, I think we should have very
little information directly in the distribution itself since it's already
quite large. It's almost as easy to have a bare-bones INSTALL file, which
would point to the wiki for additional information. But I may be very much
alone in that train of thought ; >
Post by Jay Hannah
Why isn't the short "Current events" just listed on the top of the "News"
page?
Don't know.
Post by Jay Hannah
Sick of my endless questions yet? -grin-
Not really.

cjf
Post by Jay Hannah
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Jay Hannah
2006-06-01 04:58:29 UTC
Permalink
Post by Chris Fields
Post by Jay Hannah
Is the doc/ tree being abandoned?
Most docs have been moved over to the wiki, which generates nicely formatted
docs for printing.
Oh. Well, if we've already jumped off that cliff I say we just go for it. Move everything to the wiki, nuke the empty CVS dirs, and call it good.

I hereby volunteer to strip the code out of bptutorial.pl and put it wherever. Where should I put it when I'm done? (examples/tutorial.pl?)
Post by Chris Fields
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
I believe the reasoning is along these lines: HOWTO's are focused in on
specific areas (graphics, trees, BLAST report parsing, etc) and thus usually
has greater detail. The tutorials are more broadly based (sort of a general
bioperl HOWTO). The only exception is the Beginner's HOWTO, but even that
has additional information over the tutorial (at least it did the last time
I looked at the tutorial, which has been a while).
Huh. Sounds like a subtle line. I might suggest picking one name or the other and shuffling everything into one list on the wiki.
Post by Chris Fields
Post by Jay Hannah
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on
the wiki but static?
Hence the problem we face now. It is something we need to really look into
before adding too much more to the wiki. IMHO, I think we should have very
little information directly in the distribution itself since it's already
quite large. It's almost as easy to have a bare-bones INSTALL file, which
would point to the wiki for additional information. But I may be very much
alone in that train of thought ; >
If the doc/ tree has already moved then I guess I just joined the all-wiki camp. I assume it stores full revision history and we have backups in case somebody blows something up. Any system is better than multiple systems breeding inconsistencies. Keep the spammers/clueless out and/or quickly remove their nonsense and I'm pro-wiki. Revisions email reviewers?
Post by Chris Fields
Post by Jay Hannah
Sick of my endless questions yet? -grin-
Not really.
Give it a few more posts. It'll come. :)

j
Current toy: http://openlab.jays.net/
Jay Hannah
2006-06-01 04:58:29 UTC
Permalink
Post by Chris Fields
Post by Jay Hannah
Is the doc/ tree being abandoned?
Most docs have been moved over to the wiki, which generates nicely formatted
docs for printing.
Oh. Well, if we've already jumped off that cliff I say we just go for it. Move everything to the wiki, nuke the empty CVS dirs, and call it good.

I hereby volunteer to strip the code out of bptutorial.pl and put it wherever. Where should I put it when I'm done? (examples/tutorial.pl?)
Post by Chris Fields
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
I believe the reasoning is along these lines: HOWTO's are focused in on
specific areas (graphics, trees, BLAST report parsing, etc) and thus usually
has greater detail. The tutorials are more broadly based (sort of a general
bioperl HOWTO). The only exception is the Beginner's HOWTO, but even that
has additional information over the tutorial (at least it did the last time
I looked at the tutorial, which has been a while).
Huh. Sounds like a subtle line. I might suggest picking one name or the other and shuffling everything into one list on the wiki.
Post by Chris Fields
Post by Jay Hannah
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on
the wiki but static?
Hence the problem we face now. It is something we need to really look into
before adding too much more to the wiki. IMHO, I think we should have very
little information directly in the distribution itself since it's already
quite large. It's almost as easy to have a bare-bones INSTALL file, which
would point to the wiki for additional information. But I may be very much
alone in that train of thought ; >
If the doc/ tree has already moved then I guess I just joined the all-wiki camp. I assume it stores full revision history and we have backups in case somebody blows something up. Any system is better than multiple systems breeding inconsistencies. Keep the spammers/clueless out and/or quickly remove their nonsense and I'm pro-wiki. Revisions email reviewers?
Post by Chris Fields
Post by Jay Hannah
Sick of my endless questions yet? -grin-
Not really.
Give it a few more posts. It'll come. :)

j
Current toy: http://openlab.jays.net/
Jay Hannah
2006-06-01 04:58:29 UTC
Permalink
Post by Chris Fields
Post by Jay Hannah
Is the doc/ tree being abandoned?
Most docs have been moved over to the wiki, which generates nicely formatted
docs for printing.
Oh. Well, if we've already jumped off that cliff I say we just go for it. Move everything to the wiki, nuke the empty CVS dirs, and call it good.

I hereby volunteer to strip the code out of bptutorial.pl and put it wherever. Where should I put it when I'm done? (examples/tutorial.pl?)
Post by Chris Fields
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
I believe the reasoning is along these lines: HOWTO's are focused in on
specific areas (graphics, trees, BLAST report parsing, etc) and thus usually
has greater detail. The tutorials are more broadly based (sort of a general
bioperl HOWTO). The only exception is the Beginner's HOWTO, but even that
has additional information over the tutorial (at least it did the last time
I looked at the tutorial, which has been a while).
Huh. Sounds like a subtle line. I might suggest picking one name or the other and shuffling everything into one list on the wiki.
Post by Chris Fields
Post by Jay Hannah
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on
the wiki but static?
Hence the problem we face now. It is something we need to really look into
before adding too much more to the wiki. IMHO, I think we should have very
little information directly in the distribution itself since it's already
quite large. It's almost as easy to have a bare-bones INSTALL file, which
would point to the wiki for additional information. But I may be very much
alone in that train of thought ; >
If the doc/ tree has already moved then I guess I just joined the all-wiki camp. I assume it stores full revision history and we have backups in case somebody blows something up. Any system is better than multiple systems breeding inconsistencies. Keep the spammers/clueless out and/or quickly remove their nonsense and I'm pro-wiki. Revisions email reviewers?
Post by Chris Fields
Post by Jay Hannah
Sick of my endless questions yet? -grin-
Not really.
Give it a few more posts. It'll come. :)

j
Current toy: http://openlab.jays.net/
Jay Hannah
2006-06-01 04:58:29 UTC
Permalink
Post by Chris Fields
Post by Jay Hannah
Is the doc/ tree being abandoned?
Most docs have been moved over to the wiki, which generates nicely formatted
docs for printing.
Oh. Well, if we've already jumped off that cliff I say we just go for it. Move everything to the wiki, nuke the empty CVS dirs, and call it good.

I hereby volunteer to strip the code out of bptutorial.pl and put it wherever. Where should I put it when I'm done? (examples/tutorial.pl?)
Post by Chris Fields
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
I believe the reasoning is along these lines: HOWTO's are focused in on
specific areas (graphics, trees, BLAST report parsing, etc) and thus usually
has greater detail. The tutorials are more broadly based (sort of a general
bioperl HOWTO). The only exception is the Beginner's HOWTO, but even that
has additional information over the tutorial (at least it did the last time
I looked at the tutorial, which has been a while).
Huh. Sounds like a subtle line. I might suggest picking one name or the other and shuffling everything into one list on the wiki.
Post by Chris Fields
Post by Jay Hannah
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on
the wiki but static?
Hence the problem we face now. It is something we need to really look into
before adding too much more to the wiki. IMHO, I think we should have very
little information directly in the distribution itself since it's already
quite large. It's almost as easy to have a bare-bones INSTALL file, which
would point to the wiki for additional information. But I may be very much
alone in that train of thought ; >
If the doc/ tree has already moved then I guess I just joined the all-wiki camp. I assume it stores full revision history and we have backups in case somebody blows something up. Any system is better than multiple systems breeding inconsistencies. Keep the spammers/clueless out and/or quickly remove their nonsense and I'm pro-wiki. Revisions email reviewers?
Post by Chris Fields
Post by Jay Hannah
Sick of my endless questions yet? -grin-
Not really.
Give it a few more posts. It'll come. :)

j
Current toy: http://openlab.jays.net/
Jay Hannah
2006-05-31 13:07:10 UTC
Permalink
http://www.bioperl.org/wiki/Bptutorial.pl

I think I just partially fulfilled this TODO:

TODO: check if the POD is in the Wiki yet, and if not, put it here?

I used Pod::Simple::Wiki (format 'mediawiki') to burn bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the wiki page via my web browser. (Is that proper procedure? Is the plan to just do that manually from time to time as the document changes?)

Now what?

Should there be a new link on the far left of bioperl.org called "Tutorial"?

It's an amazing document. IMHO it should be listed prominently on bioperl.org.

HTH,

j
Brian Osborne
2006-05-31 13:58:01 UTC
Permalink
Jay,

Excellent! Now we need to answer a few more questions for ourselves:

- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.

- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.

- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.

Any thoughts on these?


Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the
wiki page via my web browser. (Is that proper procedure? Is the plan to just
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called "Tutorial"?
It's an amazing document. IMHO it should be listed prominently on bioperl.org.
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-05-31 16:34:54 UTC
Permalink
Brian, Jay,

I think it would be nice to have the tutorial prominently displayed somehow
(Jay's suggestion), with a link provided via the tutorials page. Hopefully
this will help with the bioperl newbies.

Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!

Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes,
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could
be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan to
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 00:56:12 UTC
Permalink
Mauricio et al,

Sounds good, except that there are a few issues with the formatting done by
Pod::Simple::Wiki, such as changing some things to <code> tags when they
obviously aren't code; I don't know if thee is a work around for that
(Jay?). It may not be anything too serious though.

There was a similar issue with the INSTALL doc conversion to wiki that I ran
into, in that I don't think it will be easy converting one way or the other
(POD->wiki or wiki->POD or text), so syncing updates with wiki and CVS docs
could be an issue we'll have to face in the future.

We could strip the POD out of the script and have the docs on the wiki
(Brian's idea), or have minimal POD in the tutorial and keep the wiki
updated, just to simplify things, but this may not appeal to those who use
perldoc frequently (I personally use browsable prettified HTML).

cjf
-----Original Message-----
From: Mauricio Herrera Cuadra [mailto:arareko at campus.iztacala.unam.mx]
Sent: Wednesday, May 31, 2006 5:49 PM
To: Chris Fields
Cc: 'Brian Osborne'; 'Jay Hannah'; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Brian, Jay, Chris,
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
I don't think it should be a lot of problem to maintain both tutorials,
as long as the 'main' one is the one in the CVS tree. By reading what
Jay did in order to convert it into mediawiki format, I suppose this can
be easily done again for each new change to the script (again, this is
just my guessing). Besides, as far as I've seen, there aren't frequent
commits to the script at all.
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Regards,
Mauricio.
Post by Chris Fields
Brian, Jay,
I think it would be nice to have the tutorial prominently displayed
somehow
Post by Chris Fields
(Jay's suggestion), with a link provided via the tutorials page.
Hopefully
Post by Chris Fields
this will help with the bioperl newbies.
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or
more
Post by Chris Fields
spaces preceding a line denotes code for some reason). Not much you can
do
Post by Chris Fields
in these cases except remove the extra spaces in those spots. Looking
good
Post by Chris Fields
though!
Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say
yes,
Post by Chris Fields
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly
could
Post by Chris Fields
be
excised and put into the examples/ directory, for example, but this
would
Post by Chris Fields
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan
to
Post by Chris Fields
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Brian Osborne
2006-06-01 01:37:15 UTC
Permalink
Mauricio,

Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that the
documentation is more important than the script, and this is what my last
letter was asking, in part: is the script important? Or can we focus on the
text/POD part?

Brian O.


On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
Chris Fields
2006-06-01 03:09:38 UTC
Permalink
...
Post by Jay Hannah
We certainly wouldn't want to try to maintain two copies, one POD one in
wiki. That would be the worst of all options. One option that hasn't been
mentioned yet is to keep maintenance of that in POD in the distro (leaving
the cool runability alone), and then flag that document as unchangeable in
the wiki with a note on top "Maintenance of this document is done in POD
in the distro. Submit POD patches to bioperl-l and we'll re-post an
updated copy to this wiki."
Just a thought.
There are probably three schools of thought on docs: those that like nice
docs with links within and beyond BioPerl (hence the wiki), those who like
including docs with the distribution, and those that would like both. The
latter would be nice but isn't realistic unless we can come up with a way to
sync changes between the wiki and CVS those docs we want to include with the
distribution w/o too much trouble. I'm in the first school of thought since
rich text with links is better and more informative than plain text any day.
It might be a very small school though...
Post by Jay Hannah
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly
could be
Post by Brian Osborne
excised and put into the examples/ directory, for example, but this
would
Post by Brian Osborne
break a few of the paths that are being used.
scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl
I'm personally not clear on the difference. Little stuff should start in
examples/ and graduate to scripts/ once they've matured?
Is the doc/ tree being abandoned?
Most docs have been moved over to the wiki, which generates nicely formatted
docs for printing.
...
Post by Jay Hannah
Does all that stuff officially live in and is being changed in the wiki,
never to return to the distro?
It's easier to add changes in the wiki and add markup, links, etc. Much
richer text, so on.
Post by Jay Hannah
Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or
more
Post by Brian Osborne
spaces preceding a line denotes code for some reason). Not much you can
do
Post by Brian Osborne
in these cases except remove the extra spaces in those spots. Looking
good
Post by Brian Osborne
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts
didn't convert well. I've never done that conversion before, and know
nothing about mediawiki. I just blindly let Pod::Simple::Wiki do its thing
then ran off to work. :)
No big deal.
Post by Jay Hannah
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a
master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
Okay, though Mauricio may know a bit more on how/if this can be done.
Mauricio?
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
I believe the reasoning is along these lines: HOWTO's are focused in on
specific areas (graphics, trees, BLAST report parsing, etc) and thus usually
has greater detail. The tutorials are more broadly based (sort of a general
bioperl HOWTO). The only exception is the Beginner's HOWTO, but even that
has additional information over the tutorial (at least it did the last time
I looked at the tutorial, which has been a while).
Post by Jay Hannah
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on
the wiki but static?
Hence the problem we face now. It is something we need to really look into
before adding too much more to the wiki. IMHO, I think we should have very
little information directly in the distribution itself since it's already
quite large. It's almost as easy to have a bare-bones INSTALL file, which
would point to the wiki for additional information. But I may be very much
alone in that train of thought ; >
Post by Jay Hannah
Why isn't the short "Current events" just listed on the top of the "News"
page?
Don't know.
Post by Jay Hannah
Sick of my endless questions yet? -grin-
Not really.

cjf
Post by Jay Hannah
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Jay Hannah
2006-05-31 13:07:10 UTC
Permalink
http://www.bioperl.org/wiki/Bptutorial.pl

I think I just partially fulfilled this TODO:

TODO: check if the POD is in the Wiki yet, and if not, put it here?

I used Pod::Simple::Wiki (format 'mediawiki') to burn bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the wiki page via my web browser. (Is that proper procedure? Is the plan to just do that manually from time to time as the document changes?)

Now what?

Should there be a new link on the far left of bioperl.org called "Tutorial"?

It's an amazing document. IMHO it should be listed prominently on bioperl.org.

HTH,

j
Brian Osborne
2006-05-31 13:58:01 UTC
Permalink
Jay,

Excellent! Now we need to answer a few more questions for ourselves:

- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.

- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.

- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.

Any thoughts on these?


Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the
wiki page via my web browser. (Is that proper procedure? Is the plan to just
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called "Tutorial"?
It's an amazing document. IMHO it should be listed prominently on bioperl.org.
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-05-31 16:34:54 UTC
Permalink
Brian, Jay,

I think it would be nice to have the tutorial prominently displayed somehow
(Jay's suggestion), with a link provided via the tutorials page. Hopefully
this will help with the bioperl newbies.

Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!

Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes,
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could
be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan to
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 00:56:12 UTC
Permalink
Mauricio et al,

Sounds good, except that there are a few issues with the formatting done by
Pod::Simple::Wiki, such as changing some things to <code> tags when they
obviously aren't code; I don't know if thee is a work around for that
(Jay?). It may not be anything too serious though.

There was a similar issue with the INSTALL doc conversion to wiki that I ran
into, in that I don't think it will be easy converting one way or the other
(POD->wiki or wiki->POD or text), so syncing updates with wiki and CVS docs
could be an issue we'll have to face in the future.

We could strip the POD out of the script and have the docs on the wiki
(Brian's idea), or have minimal POD in the tutorial and keep the wiki
updated, just to simplify things, but this may not appeal to those who use
perldoc frequently (I personally use browsable prettified HTML).

cjf
-----Original Message-----
From: Mauricio Herrera Cuadra [mailto:arareko at campus.iztacala.unam.mx]
Sent: Wednesday, May 31, 2006 5:49 PM
To: Chris Fields
Cc: 'Brian Osborne'; 'Jay Hannah'; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Brian, Jay, Chris,
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
I don't think it should be a lot of problem to maintain both tutorials,
as long as the 'main' one is the one in the CVS tree. By reading what
Jay did in order to convert it into mediawiki format, I suppose this can
be easily done again for each new change to the script (again, this is
just my guessing). Besides, as far as I've seen, there aren't frequent
commits to the script at all.
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Regards,
Mauricio.
Post by Chris Fields
Brian, Jay,
I think it would be nice to have the tutorial prominently displayed
somehow
Post by Chris Fields
(Jay's suggestion), with a link provided via the tutorials page.
Hopefully
Post by Chris Fields
this will help with the bioperl newbies.
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or
more
Post by Chris Fields
spaces preceding a line denotes code for some reason). Not much you can
do
Post by Chris Fields
in these cases except remove the extra spaces in those spots. Looking
good
Post by Chris Fields
though!
Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say
yes,
Post by Chris Fields
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly
could
Post by Chris Fields
be
excised and put into the examples/ directory, for example, but this
would
Post by Chris Fields
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan
to
Post by Chris Fields
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Brian Osborne
2006-06-01 01:37:15 UTC
Permalink
Mauricio,

Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that the
documentation is more important than the script, and this is what my last
letter was asking, in part: is the script important? Or can we focus on the
text/POD part?

Brian O.


On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
Chris Fields
2006-06-01 03:09:38 UTC
Permalink
...
Post by Jay Hannah
We certainly wouldn't want to try to maintain two copies, one POD one in
wiki. That would be the worst of all options. One option that hasn't been
mentioned yet is to keep maintenance of that in POD in the distro (leaving
the cool runability alone), and then flag that document as unchangeable in
the wiki with a note on top "Maintenance of this document is done in POD
in the distro. Submit POD patches to bioperl-l and we'll re-post an
updated copy to this wiki."
Just a thought.
There are probably three schools of thought on docs: those that like nice
docs with links within and beyond BioPerl (hence the wiki), those who like
including docs with the distribution, and those that would like both. The
latter would be nice but isn't realistic unless we can come up with a way to
sync changes between the wiki and CVS those docs we want to include with the
distribution w/o too much trouble. I'm in the first school of thought since
rich text with links is better and more informative than plain text any day.
It might be a very small school though...
Post by Jay Hannah
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly
could be
Post by Brian Osborne
excised and put into the examples/ directory, for example, but this
would
Post by Brian Osborne
break a few of the paths that are being used.
scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl
I'm personally not clear on the difference. Little stuff should start in
examples/ and graduate to scripts/ once they've matured?
Is the doc/ tree being abandoned?
Most docs have been moved over to the wiki, which generates nicely formatted
docs for printing.
...
Post by Jay Hannah
Does all that stuff officially live in and is being changed in the wiki,
never to return to the distro?
It's easier to add changes in the wiki and add markup, links, etc. Much
richer text, so on.
Post by Jay Hannah
Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or
more
Post by Brian Osborne
spaces preceding a line denotes code for some reason). Not much you can
do
Post by Brian Osborne
in these cases except remove the extra spaces in those spots. Looking
good
Post by Brian Osborne
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts
didn't convert well. I've never done that conversion before, and know
nothing about mediawiki. I just blindly let Pod::Simple::Wiki do its thing
then ran off to work. :)
No big deal.
Post by Jay Hannah
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a
master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
Okay, though Mauricio may know a bit more on how/if this can be done.
Mauricio?
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
I believe the reasoning is along these lines: HOWTO's are focused in on
specific areas (graphics, trees, BLAST report parsing, etc) and thus usually
has greater detail. The tutorials are more broadly based (sort of a general
bioperl HOWTO). The only exception is the Beginner's HOWTO, but even that
has additional information over the tutorial (at least it did the last time
I looked at the tutorial, which has been a while).
Post by Jay Hannah
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on
the wiki but static?
Hence the problem we face now. It is something we need to really look into
before adding too much more to the wiki. IMHO, I think we should have very
little information directly in the distribution itself since it's already
quite large. It's almost as easy to have a bare-bones INSTALL file, which
would point to the wiki for additional information. But I may be very much
alone in that train of thought ; >
Post by Jay Hannah
Why isn't the short "Current events" just listed on the top of the "News"
page?
Don't know.
Post by Jay Hannah
Sick of my endless questions yet? -grin-
Not really.

cjf
Post by Jay Hannah
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Jay Hannah
2006-05-31 13:07:10 UTC
Permalink
http://www.bioperl.org/wiki/Bptutorial.pl

I think I just partially fulfilled this TODO:

TODO: check if the POD is in the Wiki yet, and if not, put it here?

I used Pod::Simple::Wiki (format 'mediawiki') to burn bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the wiki page via my web browser. (Is that proper procedure? Is the plan to just do that manually from time to time as the document changes?)

Now what?

Should there be a new link on the far left of bioperl.org called "Tutorial"?

It's an amazing document. IMHO it should be listed prominently on bioperl.org.

HTH,

j
Brian Osborne
2006-05-31 13:58:01 UTC
Permalink
Jay,

Excellent! Now we need to answer a few more questions for ourselves:

- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.

- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.

- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.

Any thoughts on these?


Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it the
wiki page via my web browser. (Is that proper procedure? Is the plan to just
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called "Tutorial"?
It's an amazing document. IMHO it should be listed prominently on bioperl.org.
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-05-31 16:34:54 UTC
Permalink
Brian, Jay,

I think it would be nice to have the tutorial prominently displayed somehow
(Jay's suggestion), with a link provided via the tutorials page. Hopefully
this will help with the bioperl newbies.

Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!

Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say yes,
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly could
be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan to
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 16:20:34 UTC
Permalink
Sounds good to me. I guess the tutorial (post-stripping)would be moved to
/scripts or /examples then?

Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?

Chris
-----Original Message-----
From: Mauricio Herrera Cuadra [mailto:arareko at campus.iztacala.unam.mx]
Sent: Thursday, June 01, 2006 11:13 AM
To: Brian Osborne
Cc: Chris Fields; bioperl-l at lists.open-bio.org; 'Jay Hannah'
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
You're right Brian. I also think that the text/POD part is more
important than the script. Since we're more into moving everything to
the Wiki, I believe this would be the right approach.
Moving the script part of the tutorial into the examples/ directory is
also a nice idea.
Mauricio.
Post by Brian Osborne
Mauricio,
Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that
the
Post by Brian Osborne
documentation is more important than the script, and this is what my
last
Post by Brian Osborne
letter was asking, in part: is the script important? Or can we focus on
the
Post by Brian Osborne
text/POD part?
Brian O.
On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Sendu Bala
2006-06-01 16:57:27 UTC
Permalink
Post by Chris Fields
Sounds good to me. I guess the tutorial (post-stripping)would be moved to
/scripts or /examples then?
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?
Imho, something like an installation document should be there in full so
once you've downloaded you can install without reference to anything
else. Also, an installation document could be considered specific to the
release version. Which is to say, it never goes out of date even if new
versions of bioperl are released with new installation instructions - it
applies to the installation directory it is found in.

The wiki can have the latest installation instructions, and you don't
have to worry about keeping things synced.
Sendu Bala
2006-06-01 16:57:27 UTC
Permalink
Post by Chris Fields
Sounds good to me. I guess the tutorial (post-stripping)would be moved to
/scripts or /examples then?
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?
Imho, something like an installation document should be there in full so
once you've downloaded you can install without reference to anything
else. Also, an installation document could be considered specific to the
release version. Which is to say, it never goes out of date even if new
versions of bioperl are released with new installation instructions - it
applies to the installation directory it is found in.

The wiki can have the latest installation instructions, and you don't
have to worry about keeping things synced.
Sendu Bala
2006-06-01 16:57:27 UTC
Permalink
Post by Chris Fields
Sounds good to me. I guess the tutorial (post-stripping)would be moved to
/scripts or /examples then?
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?
Imho, something like an installation document should be there in full so
once you've downloaded you can install without reference to anything
else. Also, an installation document could be considered specific to the
release version. Which is to say, it never goes out of date even if new
versions of bioperl are released with new installation instructions - it
applies to the installation directory it is found in.

The wiki can have the latest installation instructions, and you don't
have to worry about keeping things synced.
Sendu Bala
2006-06-01 16:57:27 UTC
Permalink
Post by Chris Fields
Sounds good to me. I guess the tutorial (post-stripping)would be moved to
/scripts or /examples then?
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?
Imho, something like an installation document should be there in full so
once you've downloaded you can install without reference to anything
else. Also, an installation document could be considered specific to the
release version. Which is to say, it never goes out of date even if new
versions of bioperl are released with new installation instructions - it
applies to the installation directory it is found in.

The wiki can have the latest installation instructions, and you don't
have to worry about keeping things synced.
Brian Osborne
2006-06-01 16:46:02 UTC
Permalink
Chris,

I think the INSTALL* files should be in the package, this is the de facto
convention for 99% of the packages I've ever seen. Then any Wiki page just
links to the file in CVS.

Personally I don't like the idea of maintaining a Wiki page and a file that
both say essentially the same thing (this is what has happened with the
INSTALL and INSTALL.WIN files). I've spent plenty of time merging redundant
text and removing files that contained these redundancies so it's
unfortunate to see them appear anew, sooner or later they'll get out of sync
despite best intentions. The most likely cause will be someone other than
the person who created the initial duplication (and promised to maintain
both) making a change in one of the two files.

Brian O.
Post by Chris Fields
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?
Chris Fields
2006-06-01 17:13:30 UTC
Permalink
So basically have a minimal set of installation instructions in CVS and a
more detailed installation instructions on the wiki. Sounds reasonable
enough but bioperl is a pretty complex distribution (lots of additional
modules required, platform-specific issues, so on). Maybe we can come up
with a pared-down INSTALL file which combines the basic elements for
installing on UNIX/Windows/Mac/FreeBSD and points out dependencies.

I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).

Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Sendu Bala
Sent: Thursday, June 01, 2006 11:57 AM
To: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Post by Chris Fields
Sounds good to me. I guess the tutorial (post-stripping)would be moved
to
Post by Chris Fields
/scripts or /examples then?
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in
the
Post by Chris Fields
distribution pointing out the wiki docs instead?
Imho, something like an installation document should be there in full so
once you've downloaded you can install without reference to anything
else. Also, an installation document could be considered specific to the
release version. Which is to say, it never goes out of date even if new
versions of bioperl are released with new installation instructions - it
applies to the installation directory it is found in.
The wiki can have the latest installation instructions, and you don't
have to worry about keeping things synced.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 17:46:35 UTC
Permalink
I understand your point, though I think the wiki gives us an opportunity add
helpful links and use markup to help clarify things a bit more. I have seen
several distributions which don't have INSTALL files, just simple README
with very basic instructions (Bio::ASN1::EntrezGene is one).

I've been reluctant to mess around with the wiki Install pages too much more
b/c of syncing problems, just as you mentioned. I will look into thing a
bit more to see if there's an easier way to go about converting wiki->text.

Chris
-----Original Message-----
From: Brian Osborne [mailto:osborne1 at optonline.net]
Sent: Thursday, June 01, 2006 11:46 AM
To: Chris Fields; 'Mauricio Herrera Cuadra'
Cc: bioperl-l at lists.open-bio.org; 'Jay Hannah'
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Chris,
I think the INSTALL* files should be in the package, this is the de facto
convention for 99% of the packages I've ever seen. Then any Wiki page just
links to the file in CVS.
Personally I don't like the idea of maintaining a Wiki page and a file
that
both say essentially the same thing (this is what has happened with the
INSTALL and INSTALL.WIN files). I've spent plenty of time merging
redundant
text and removing files that contained these redundancies so it's
unfortunate to see them appear anew, sooner or later they'll get out of
sync
despite best intentions. The most likely cause will be someone other than
the person who created the initial duplication (and promised to maintain
both) making a change in one of the two files.
Brian O.
Post by Chris Fields
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in
the
Post by Chris Fields
distribution pointing out the wiki docs instead?
Brian Osborne
2006-06-01 19:36:27 UTC
Permalink
Chris,

Right - how would this be done?

Brian O.
Post by Chris Fields
I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).
Brian Osborne
2006-06-01 19:44:13 UTC
Permalink
Jay,

You asked about the doc/ directory. The only directory I see in my
bioperl-live/doc directory is examples/, the reason this remains is that it
contains scripts and images related to the Graphics HOWTO, in theory these
could be moved to the Wiki and the examples/ directory deleted. One
explanation for why you see doc/html and all those other dirs is that you
aren't using the 'cvs -d' option (there are other explanations) when you
update.

If examples/ is removed then presumably the README can be removed and
makedoc.pl moved elsewhere.

Brian O.
Post by Jay Hannah
Post by Brian Osborne
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
We certainly wouldn't want to try to maintain two copies, one POD one in wiki.
That would be the worst of all options. One option that hasn't been mentioned
yet is to keep maintenance of that in POD in the distro (leaving the cool
runability alone), and then flag that document as unchangeable in the wiki
with a note on top "Maintenance of this document is done in POD in the distro.
Submit POD patches to bioperl-l and we'll re-post an updated copy to this
wiki."
Just a thought.
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl
I'm personally not clear on the difference. Little stuff should start in
examples/ and graduate to scripts/ once they've matured?
Is the doc/ tree being abandoned?
doc/faq (empty?)
doc/howto
doc/howto/examples
doc/howto/figs (empty?)
doc/howto/html (empty?)
doc/howto/pdf (empty?)
doc/howto/sgml (empty?)
doc/howto/txt (empty?)
doc/howto/xml (empty?)
Does all that stuff officially live in and is being changed in the wiki, never
to return to the distro?
Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts
didn't convert well. I've never done that conversion before, and know nothing
about mediawiki. I just blindly let Pod::Simple::Wiki do its thing then ran
off to work. :)
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a
master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
(What's the conceptual difference between a HOWTO and a tutorial?)
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on the
wiki but static?
Why isn't the short "Current events" just listed on the top of the "News"
page?
Sick of my endless questions yet? -grin-
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 19:47:40 UTC
Permalink
-----Original Message-----
From: Brian Osborne [mailto:osborne1 at optonline.net]
Sent: Thursday, June 01, 2006 2:36 PM
To: Chris Fields; 'Sendu Bala'; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Chris,
Right - how would this be done?
I'll look into a few of the wiki converters, there are a few things that
claim to convert wiki to other formats (and vice versa). It may not be
direct, though. I'll post anything if I figure something out.

Chris
Brian O.
Post by Chris Fields
I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).
Brian Osborne
2006-06-01 19:45:39 UTC
Permalink
Jay,

Yes, good idea, thank you for volunteering.

Brian O.
Post by Jay Hannah
I hereby volunteer to strip the code out of bptutorial.pl and put it wherever.
Where should I put it when I'm done? (examples/tutorial.pl?)
Chris Fields
2006-06-01 16:20:34 UTC
Permalink
Sounds good to me. I guess the tutorial (post-stripping)would be moved to
/scripts or /examples then?

Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?

Chris
-----Original Message-----
From: Mauricio Herrera Cuadra [mailto:arareko at campus.iztacala.unam.mx]
Sent: Thursday, June 01, 2006 11:13 AM
To: Brian Osborne
Cc: Chris Fields; bioperl-l at lists.open-bio.org; 'Jay Hannah'
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
You're right Brian. I also think that the text/POD part is more
important than the script. Since we're more into moving everything to
the Wiki, I believe this would be the right approach.
Moving the script part of the tutorial into the examples/ directory is
also a nice idea.
Mauricio.
Post by Brian Osborne
Mauricio,
Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that
the
Post by Brian Osborne
documentation is more important than the script, and this is what my
last
Post by Brian Osborne
letter was asking, in part: is the script important? Or can we focus on
the
Post by Brian Osborne
text/POD part?
Brian O.
On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Brian Osborne
2006-06-01 16:46:02 UTC
Permalink
Chris,

I think the INSTALL* files should be in the package, this is the de facto
convention for 99% of the packages I've ever seen. Then any Wiki page just
links to the file in CVS.

Personally I don't like the idea of maintaining a Wiki page and a file that
both say essentially the same thing (this is what has happened with the
INSTALL and INSTALL.WIN files). I've spent plenty of time merging redundant
text and removing files that contained these redundancies so it's
unfortunate to see them appear anew, sooner or later they'll get out of sync
despite best intentions. The most likely cause will be someone other than
the person who created the initial duplication (and promised to maintain
both) making a change in one of the two files.

Brian O.
Post by Chris Fields
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?
Chris Fields
2006-06-01 17:13:30 UTC
Permalink
So basically have a minimal set of installation instructions in CVS and a
more detailed installation instructions on the wiki. Sounds reasonable
enough but bioperl is a pretty complex distribution (lots of additional
modules required, platform-specific issues, so on). Maybe we can come up
with a pared-down INSTALL file which combines the basic elements for
installing on UNIX/Windows/Mac/FreeBSD and points out dependencies.

I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).

Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Sendu Bala
Sent: Thursday, June 01, 2006 11:57 AM
To: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Post by Chris Fields
Sounds good to me. I guess the tutorial (post-stripping)would be moved
to
Post by Chris Fields
/scripts or /examples then?
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in
the
Post by Chris Fields
distribution pointing out the wiki docs instead?
Imho, something like an installation document should be there in full so
once you've downloaded you can install without reference to anything
else. Also, an installation document could be considered specific to the
release version. Which is to say, it never goes out of date even if new
versions of bioperl are released with new installation instructions - it
applies to the installation directory it is found in.
The wiki can have the latest installation instructions, and you don't
have to worry about keeping things synced.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 17:46:35 UTC
Permalink
I understand your point, though I think the wiki gives us an opportunity add
helpful links and use markup to help clarify things a bit more. I have seen
several distributions which don't have INSTALL files, just simple README
with very basic instructions (Bio::ASN1::EntrezGene is one).

I've been reluctant to mess around with the wiki Install pages too much more
b/c of syncing problems, just as you mentioned. I will look into thing a
bit more to see if there's an easier way to go about converting wiki->text.

Chris
-----Original Message-----
From: Brian Osborne [mailto:osborne1 at optonline.net]
Sent: Thursday, June 01, 2006 11:46 AM
To: Chris Fields; 'Mauricio Herrera Cuadra'
Cc: bioperl-l at lists.open-bio.org; 'Jay Hannah'
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Chris,
I think the INSTALL* files should be in the package, this is the de facto
convention for 99% of the packages I've ever seen. Then any Wiki page just
links to the file in CVS.
Personally I don't like the idea of maintaining a Wiki page and a file
that
both say essentially the same thing (this is what has happened with the
INSTALL and INSTALL.WIN files). I've spent plenty of time merging
redundant
text and removing files that contained these redundancies so it's
unfortunate to see them appear anew, sooner or later they'll get out of
sync
despite best intentions. The most likely cause will be someone other than
the person who created the initial duplication (and promised to maintain
both) making a change in one of the two files.
Brian O.
Post by Chris Fields
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in
the
Post by Chris Fields
distribution pointing out the wiki docs instead?
Brian Osborne
2006-06-01 19:36:27 UTC
Permalink
Chris,

Right - how would this be done?

Brian O.
Post by Chris Fields
I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).
Brian Osborne
2006-06-01 19:44:13 UTC
Permalink
Jay,

You asked about the doc/ directory. The only directory I see in my
bioperl-live/doc directory is examples/, the reason this remains is that it
contains scripts and images related to the Graphics HOWTO, in theory these
could be moved to the Wiki and the examples/ directory deleted. One
explanation for why you see doc/html and all those other dirs is that you
aren't using the 'cvs -d' option (there are other explanations) when you
update.

If examples/ is removed then presumably the README can be removed and
makedoc.pl moved elsewhere.

Brian O.
Post by Jay Hannah
Post by Brian Osborne
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
We certainly wouldn't want to try to maintain two copies, one POD one in wiki.
That would be the worst of all options. One option that hasn't been mentioned
yet is to keep maintenance of that in POD in the distro (leaving the cool
runability alone), and then flag that document as unchangeable in the wiki
with a note on top "Maintenance of this document is done in POD in the distro.
Submit POD patches to bioperl-l and we'll re-post an updated copy to this
wiki."
Just a thought.
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl
I'm personally not clear on the difference. Little stuff should start in
examples/ and graduate to scripts/ once they've matured?
Is the doc/ tree being abandoned?
doc/faq (empty?)
doc/howto
doc/howto/examples
doc/howto/figs (empty?)
doc/howto/html (empty?)
doc/howto/pdf (empty?)
doc/howto/sgml (empty?)
doc/howto/txt (empty?)
doc/howto/xml (empty?)
Does all that stuff officially live in and is being changed in the wiki, never
to return to the distro?
Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts
didn't convert well. I've never done that conversion before, and know nothing
about mediawiki. I just blindly let Pod::Simple::Wiki do its thing then ran
off to work. :)
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a
master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
(What's the conceptual difference between a HOWTO and a tutorial?)
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on the
wiki but static?
Why isn't the short "Current events" just listed on the top of the "News"
page?
Sick of my endless questions yet? -grin-
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 19:47:40 UTC
Permalink
-----Original Message-----
From: Brian Osborne [mailto:osborne1 at optonline.net]
Sent: Thursday, June 01, 2006 2:36 PM
To: Chris Fields; 'Sendu Bala'; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Chris,
Right - how would this be done?
I'll look into a few of the wiki converters, there are a few things that
claim to convert wiki to other formats (and vice versa). It may not be
direct, though. I'll post anything if I figure something out.

Chris
Brian O.
Post by Chris Fields
I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).
Brian Osborne
2006-06-01 19:45:39 UTC
Permalink
Jay,

Yes, good idea, thank you for volunteering.

Brian O.
Post by Jay Hannah
I hereby volunteer to strip the code out of bptutorial.pl and put it wherever.
Where should I put it when I'm done? (examples/tutorial.pl?)
Chris Fields
2006-06-01 16:20:34 UTC
Permalink
Sounds good to me. I guess the tutorial (post-stripping)would be moved to
/scripts or /examples then?

Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?

Chris
-----Original Message-----
From: Mauricio Herrera Cuadra [mailto:arareko at campus.iztacala.unam.mx]
Sent: Thursday, June 01, 2006 11:13 AM
To: Brian Osborne
Cc: Chris Fields; bioperl-l at lists.open-bio.org; 'Jay Hannah'
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
You're right Brian. I also think that the text/POD part is more
important than the script. Since we're more into moving everything to
the Wiki, I believe this would be the right approach.
Moving the script part of the tutorial into the examples/ directory is
also a nice idea.
Mauricio.
Post by Brian Osborne
Mauricio,
Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that
the
Post by Brian Osborne
documentation is more important than the script, and this is what my
last
Post by Brian Osborne
letter was asking, in part: is the script important? Or can we focus on
the
Post by Brian Osborne
text/POD part?
Brian O.
On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Brian Osborne
2006-06-01 16:46:02 UTC
Permalink
Chris,

I think the INSTALL* files should be in the package, this is the de facto
convention for 99% of the packages I've ever seen. Then any Wiki page just
links to the file in CVS.

Personally I don't like the idea of maintaining a Wiki page and a file that
both say essentially the same thing (this is what has happened with the
INSTALL and INSTALL.WIN files). I've spent plenty of time merging redundant
text and removing files that contained these redundancies so it's
unfortunate to see them appear anew, sooner or later they'll get out of sync
despite best intentions. The most likely cause will be someone other than
the person who created the initial duplication (and promised to maintain
both) making a change in one of the two files.

Brian O.
Post by Chris Fields
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?
Chris Fields
2006-06-01 17:13:30 UTC
Permalink
So basically have a minimal set of installation instructions in CVS and a
more detailed installation instructions on the wiki. Sounds reasonable
enough but bioperl is a pretty complex distribution (lots of additional
modules required, platform-specific issues, so on). Maybe we can come up
with a pared-down INSTALL file which combines the basic elements for
installing on UNIX/Windows/Mac/FreeBSD and points out dependencies.

I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).

Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Sendu Bala
Sent: Thursday, June 01, 2006 11:57 AM
To: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Post by Chris Fields
Sounds good to me. I guess the tutorial (post-stripping)would be moved
to
Post by Chris Fields
/scripts or /examples then?
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in
the
Post by Chris Fields
distribution pointing out the wiki docs instead?
Imho, something like an installation document should be there in full so
once you've downloaded you can install without reference to anything
else. Also, an installation document could be considered specific to the
release version. Which is to say, it never goes out of date even if new
versions of bioperl are released with new installation instructions - it
applies to the installation directory it is found in.
The wiki can have the latest installation instructions, and you don't
have to worry about keeping things synced.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 17:46:35 UTC
Permalink
I understand your point, though I think the wiki gives us an opportunity add
helpful links and use markup to help clarify things a bit more. I have seen
several distributions which don't have INSTALL files, just simple README
with very basic instructions (Bio::ASN1::EntrezGene is one).

I've been reluctant to mess around with the wiki Install pages too much more
b/c of syncing problems, just as you mentioned. I will look into thing a
bit more to see if there's an easier way to go about converting wiki->text.

Chris
-----Original Message-----
From: Brian Osborne [mailto:osborne1 at optonline.net]
Sent: Thursday, June 01, 2006 11:46 AM
To: Chris Fields; 'Mauricio Herrera Cuadra'
Cc: bioperl-l at lists.open-bio.org; 'Jay Hannah'
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Chris,
I think the INSTALL* files should be in the package, this is the de facto
convention for 99% of the packages I've ever seen. Then any Wiki page just
links to the file in CVS.
Personally I don't like the idea of maintaining a Wiki page and a file
that
both say essentially the same thing (this is what has happened with the
INSTALL and INSTALL.WIN files). I've spent plenty of time merging
redundant
text and removing files that contained these redundancies so it's
unfortunate to see them appear anew, sooner or later they'll get out of
sync
despite best intentions. The most likely cause will be someone other than
the person who created the initial duplication (and promised to maintain
both) making a change in one of the two files.
Brian O.
Post by Chris Fields
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in
the
Post by Chris Fields
distribution pointing out the wiki docs instead?
Brian Osborne
2006-06-01 19:36:27 UTC
Permalink
Chris,

Right - how would this be done?

Brian O.
Post by Chris Fields
I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).
Brian Osborne
2006-06-01 19:44:13 UTC
Permalink
Jay,

You asked about the doc/ directory. The only directory I see in my
bioperl-live/doc directory is examples/, the reason this remains is that it
contains scripts and images related to the Graphics HOWTO, in theory these
could be moved to the Wiki and the examples/ directory deleted. One
explanation for why you see doc/html and all those other dirs is that you
aren't using the 'cvs -d' option (there are other explanations) when you
update.

If examples/ is removed then presumably the README can be removed and
makedoc.pl moved elsewhere.

Brian O.
Post by Jay Hannah
Post by Brian Osborne
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
We certainly wouldn't want to try to maintain two copies, one POD one in wiki.
That would be the worst of all options. One option that hasn't been mentioned
yet is to keep maintenance of that in POD in the distro (leaving the cool
runability alone), and then flag that document as unchangeable in the wiki
with a note on top "Maintenance of this document is done in POD in the distro.
Submit POD patches to bioperl-l and we'll re-post an updated copy to this
wiki."
Just a thought.
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl
I'm personally not clear on the difference. Little stuff should start in
examples/ and graduate to scripts/ once they've matured?
Is the doc/ tree being abandoned?
doc/faq (empty?)
doc/howto
doc/howto/examples
doc/howto/figs (empty?)
doc/howto/html (empty?)
doc/howto/pdf (empty?)
doc/howto/sgml (empty?)
doc/howto/txt (empty?)
doc/howto/xml (empty?)
Does all that stuff officially live in and is being changed in the wiki, never
to return to the distro?
Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts
didn't convert well. I've never done that conversion before, and know nothing
about mediawiki. I just blindly let Pod::Simple::Wiki do its thing then ran
off to work. :)
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a
master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
(What's the conceptual difference between a HOWTO and a tutorial?)
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on the
wiki but static?
Why isn't the short "Current events" just listed on the top of the "News"
page?
Sick of my endless questions yet? -grin-
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 19:47:40 UTC
Permalink
-----Original Message-----
From: Brian Osborne [mailto:osborne1 at optonline.net]
Sent: Thursday, June 01, 2006 2:36 PM
To: Chris Fields; 'Sendu Bala'; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Chris,
Right - how would this be done?
I'll look into a few of the wiki converters, there are a few things that
claim to convert wiki to other formats (and vice versa). It may not be
direct, though. I'll post anything if I figure something out.

Chris
Brian O.
Post by Chris Fields
I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).
Brian Osborne
2006-06-01 19:45:39 UTC
Permalink
Jay,

Yes, good idea, thank you for volunteering.

Brian O.
Post by Jay Hannah
I hereby volunteer to strip the code out of bptutorial.pl and put it wherever.
Where should I put it when I'm done? (examples/tutorial.pl?)
Chris Fields
2006-06-01 00:56:12 UTC
Permalink
Mauricio et al,

Sounds good, except that there are a few issues with the formatting done by
Pod::Simple::Wiki, such as changing some things to <code> tags when they
obviously aren't code; I don't know if thee is a work around for that
(Jay?). It may not be anything too serious though.

There was a similar issue with the INSTALL doc conversion to wiki that I ran
into, in that I don't think it will be easy converting one way or the other
(POD->wiki or wiki->POD or text), so syncing updates with wiki and CVS docs
could be an issue we'll have to face in the future.

We could strip the POD out of the script and have the docs on the wiki
(Brian's idea), or have minimal POD in the tutorial and keep the wiki
updated, just to simplify things, but this may not appeal to those who use
perldoc frequently (I personally use browsable prettified HTML).

cjf
-----Original Message-----
From: Mauricio Herrera Cuadra [mailto:arareko at campus.iztacala.unam.mx]
Sent: Wednesday, May 31, 2006 5:49 PM
To: Chris Fields
Cc: 'Brian Osborne'; 'Jay Hannah'; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Brian, Jay, Chris,
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
I don't think it should be a lot of problem to maintain both tutorials,
as long as the 'main' one is the one in the CVS tree. By reading what
Jay did in order to convert it into mediawiki format, I suppose this can
be easily done again for each new change to the script (again, this is
just my guessing). Besides, as far as I've seen, there aren't frequent
commits to the script at all.
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Regards,
Mauricio.
Post by Chris Fields
Brian, Jay,
I think it would be nice to have the tutorial prominently displayed
somehow
Post by Chris Fields
(Jay's suggestion), with a link provided via the tutorials page.
Hopefully
Post by Chris Fields
this will help with the bioperl newbies.
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or
more
Post by Chris Fields
spaces preceding a line denotes code for some reason). Not much you can
do
Post by Chris Fields
in these cases except remove the extra spaces in those spots. Looking
good
Post by Chris Fields
though!
Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Brian Osborne
Sent: Wednesday, May 31, 2006 8:58 AM
To: Jay Hannah; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Jay,
- Do we remove the file bptutorial.pl from the package now? I'd say
yes,
Post by Chris Fields
we
don't want to have to maintain two bptutorials.
- What do we do with the script part of bptutorial.pl? It certainly
could
Post by Chris Fields
be
excised and put into the examples/ directory, for example, but this
would
Post by Chris Fields
break a few of the paths that are being used.
- A link to bptutorial? Or a link to the existing tutorials page?
http://www.bioperl.org/wiki/Tutorials.
Any thoughts on these?
Brian O.
Post by Jay Hannah
http://www.bioperl.org/wiki/Bptutorial.pl
TODO: check if the POD is in the Wiki yet, and if not, put it here?
I used Pod::Simple::Wiki (format 'mediawiki') to burn
bioperl-live/bptutorial.pl POD into mediawiki format. I then pasted it
the
Post by Jay Hannah
wiki page via my web browser. (Is that proper procedure? Is the plan
to
Post by Chris Fields
just
Post by Jay Hannah
do that manually from time to time as the document changes?)
Now what?
Should there be a new link on the far left of bioperl.org called
"Tutorial"?
Post by Jay Hannah
It's an amazing document. IMHO it should be listed prominently on
bioperl.org.
Post by Jay Hannah
HTH,
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Brian Osborne
2006-06-01 01:37:15 UTC
Permalink
Mauricio,

Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that the
documentation is more important than the script, and this is what my last
letter was asking, in part: is the script important? Or can we focus on the
text/POD part?

Brian O.


On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
Chris Fields
2006-06-01 03:09:38 UTC
Permalink
...
Post by Jay Hannah
We certainly wouldn't want to try to maintain two copies, one POD one in
wiki. That would be the worst of all options. One option that hasn't been
mentioned yet is to keep maintenance of that in POD in the distro (leaving
the cool runability alone), and then flag that document as unchangeable in
the wiki with a note on top "Maintenance of this document is done in POD
in the distro. Submit POD patches to bioperl-l and we'll re-post an
updated copy to this wiki."
Just a thought.
There are probably three schools of thought on docs: those that like nice
docs with links within and beyond BioPerl (hence the wiki), those who like
including docs with the distribution, and those that would like both. The
latter would be nice but isn't realistic unless we can come up with a way to
sync changes between the wiki and CVS those docs we want to include with the
distribution w/o too much trouble. I'm in the first school of thought since
rich text with links is better and more informative than plain text any day.
It might be a very small school though...
Post by Jay Hannah
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly
could be
Post by Brian Osborne
excised and put into the examples/ directory, for example, but this
would
Post by Brian Osborne
break a few of the paths that are being used.
scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl
I'm personally not clear on the difference. Little stuff should start in
examples/ and graduate to scripts/ once they've matured?
Is the doc/ tree being abandoned?
Most docs have been moved over to the wiki, which generates nicely formatted
docs for printing.
...
Post by Jay Hannah
Does all that stuff officially live in and is being changed in the wiki,
never to return to the distro?
It's easier to add changes in the wiki and add markup, links, etc. Much
richer text, so on.
Post by Jay Hannah
Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or
more
Post by Brian Osborne
spaces preceding a line denotes code for some reason). Not much you can
do
Post by Brian Osborne
in these cases except remove the extra spaces in those spots. Looking
good
Post by Brian Osborne
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts
didn't convert well. I've never done that conversion before, and know
nothing about mediawiki. I just blindly let Pod::Simple::Wiki do its thing
then ran off to work. :)
No big deal.
Post by Jay Hannah
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a
master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
Okay, though Mauricio may know a bit more on how/if this can be done.
Mauricio?
Post by Jay Hannah
(What's the conceptual difference between a HOWTO and a tutorial?)
I believe the reasoning is along these lines: HOWTO's are focused in on
specific areas (graphics, trees, BLAST report parsing, etc) and thus usually
has greater detail. The tutorials are more broadly based (sort of a general
bioperl HOWTO). The only exception is the Beginner's HOWTO, but even that
has additional information over the tutorial (at least it did the last time
I looked at the tutorial, which has been a while).
Post by Jay Hannah
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on
the wiki but static?
Hence the problem we face now. It is something we need to really look into
before adding too much more to the wiki. IMHO, I think we should have very
little information directly in the distribution itself since it's already
quite large. It's almost as easy to have a bare-bones INSTALL file, which
would point to the wiki for additional information. But I may be very much
alone in that train of thought ; >
Post by Jay Hannah
Why isn't the short "Current events" just listed on the top of the "News"
page?
Don't know.
Post by Jay Hannah
Sick of my endless questions yet? -grin-
Not really.

cjf
Post by Jay Hannah
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 16:20:34 UTC
Permalink
Sounds good to me. I guess the tutorial (post-stripping)would be moved to
/scripts or /examples then?

Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?

Chris
-----Original Message-----
From: Mauricio Herrera Cuadra [mailto:arareko at campus.iztacala.unam.mx]
Sent: Thursday, June 01, 2006 11:13 AM
To: Brian Osborne
Cc: Chris Fields; bioperl-l at lists.open-bio.org; 'Jay Hannah'
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
You're right Brian. I also think that the text/POD part is more
important than the script. Since we're more into moving everything to
the Wiki, I believe this would be the right approach.
Moving the script part of the tutorial into the examples/ directory is
also a nice idea.
Mauricio.
Post by Brian Osborne
Mauricio,
Bernd didn't say he want the _script_ in the package, he said he wanted
bptutorial.pl in the package, not indicating whether it was the
documentation or the script that was important. It's my suspicion that
the
Post by Brian Osborne
documentation is more important than the script, and this is what my
last
Post by Brian Osborne
letter was asking, in part: is the script important? Or can we focus on
the
Post by Brian Osborne
text/POD part?
Brian O.
On 5/31/06 6:49 PM, "Mauricio Herrera Cuadra"
Post by Mauricio Herrera Cuadra
I agree with what Bernd Web said in another reply. For some people will
be nice to still be able to run the script from the codebase and
interact with it.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
--
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM
Brian Osborne
2006-06-01 16:46:02 UTC
Permalink
Chris,

I think the INSTALL* files should be in the package, this is the de facto
convention for 99% of the packages I've ever seen. Then any Wiki page just
links to the file in CVS.

Personally I don't like the idea of maintaining a Wiki page and a file that
both say essentially the same thing (this is what has happened with the
INSTALL and INSTALL.WIN files). I've spent plenty of time merging redundant
text and removing files that contained these redundancies so it's
unfortunate to see them appear anew, sooner or later they'll get out of sync
despite best intentions. The most likely cause will be someone other than
the person who created the initial duplication (and promised to maintain
both) making a change in one of the two files.

Brian O.
Post by Chris Fields
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in the
distribution pointing out the wiki docs instead?
Chris Fields
2006-06-01 17:13:30 UTC
Permalink
So basically have a minimal set of installation instructions in CVS and a
more detailed installation instructions on the wiki. Sounds reasonable
enough but bioperl is a pretty complex distribution (lots of additional
modules required, platform-specific issues, so on). Maybe we can come up
with a pared-down INSTALL file which combines the basic elements for
installing on UNIX/Windows/Mac/FreeBSD and points out dependencies.

I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).

Chris
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
bounces at lists.open-bio.org] On Behalf Of Sendu Bala
Sent: Thursday, June 01, 2006 11:57 AM
To: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Post by Chris Fields
Sounds good to me. I guess the tutorial (post-stripping)would be moved
to
Post by Chris Fields
/scripts or /examples then?
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in
the
Post by Chris Fields
distribution pointing out the wiki docs instead?
Imho, something like an installation document should be there in full so
once you've downloaded you can install without reference to anything
else. Also, an installation document could be considered specific to the
release version. Which is to say, it never goes out of date even if new
versions of bioperl are released with new installation instructions - it
applies to the installation directory it is found in.
The wiki can have the latest installation instructions, and you don't
have to worry about keeping things synced.
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Chris Fields
2006-06-01 17:46:35 UTC
Permalink
I understand your point, though I think the wiki gives us an opportunity add
helpful links and use markup to help clarify things a bit more. I have seen
several distributions which don't have INSTALL files, just simple README
with very basic instructions (Bio::ASN1::EntrezGene is one).

I've been reluctant to mess around with the wiki Install pages too much more
b/c of syncing problems, just as you mentioned. I will look into thing a
bit more to see if there's an easier way to go about converting wiki->text.

Chris
-----Original Message-----
From: Brian Osborne [mailto:osborne1 at optonline.net]
Sent: Thursday, June 01, 2006 11:46 AM
To: Chris Fields; 'Mauricio Herrera Cuadra'
Cc: bioperl-l at lists.open-bio.org; 'Jay Hannah'
Subject: Re: [Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl
Chris,
I think the INSTALL* files should be in the package, this is the de facto
convention for 99% of the packages I've ever seen. Then any Wiki page just
links to the file in CVS.
Personally I don't like the idea of maintaining a Wiki page and a file
that
both say essentially the same thing (this is what has happened with the
INSTALL and INSTALL.WIN files). I've spent plenty of time merging
redundant
text and removing files that contained these redundancies so it's
unfortunate to see them appear anew, sooner or later they'll get out of
sync
despite best intentions. The most likely cause will be someone other than
the person who created the initial duplication (and promised to maintain
both) making a change in one of the two files.
Brian O.
Post by Chris Fields
Also, what do we do about similar situation with other docs moved to the
wiki (INSTALL, INSTALL.WIN, etc)? Should we have a placeholder file in
the
Post by Chris Fields
distribution pointing out the wiki docs instead?
Brian Osborne
2006-06-01 19:36:27 UTC
Permalink
Chris,

Right - how would this be done?

Brian O.
Post by Chris Fields
I still like the idea of just having a simple conversion from wiki->txt
direct from the web page (i.e. best of both worlds).
Brian Osborne
2006-06-01 19:44:13 UTC
Permalink
Jay,

You asked about the doc/ directory. The only directory I see in my
bioperl-live/doc directory is examples/, the reason this remains is that it
contains scripts and images related to the Graphics HOWTO, in theory these
could be moved to the Wiki and the examples/ directory deleted. One
explanation for why you see doc/html and all those other dirs is that you
aren't using the 'cvs -d' option (there are other explanations) when you
update.

If examples/ is removed then presumably the README can be removed and
makedoc.pl moved elsewhere.

Brian O.
Post by Jay Hannah
Post by Brian Osborne
- Do we remove the file bptutorial.pl from the package now? I'd say yes, we
don't want to have to maintain two bptutorials.
We certainly wouldn't want to try to maintain two copies, one POD one in wiki.
That would be the worst of all options. One option that hasn't been mentioned
yet is to keep maintenance of that in POD in the distro (leaving the cool
runability alone), and then flag that document as unchangeable in the wiki
with a note on top "Maintenance of this document is done in POD in the distro.
Submit POD patches to bioperl-l and we'll re-post an updated copy to this
wiki."
Just a thought.
Post by Brian Osborne
- What do we do with the script part of bptutorial.pl? It certainly could be
excised and put into the examples/ directory, for example, but this would
break a few of the paths that are being used.
scripts/ - Useful production-quality scripts with POD documentation
examples/ - Scripts demonstrating the many uses of Bioperl
I'm personally not clear on the difference. Little stuff should start in
examples/ and graduate to scripts/ once they've matured?
Is the doc/ tree being abandoned?
doc/faq (empty?)
doc/howto
doc/howto/examples
doc/howto/figs (empty?)
doc/howto/html (empty?)
doc/howto/pdf (empty?)
doc/howto/sgml (empty?)
doc/howto/txt (empty?)
doc/howto/xml (empty?)
Does all that stuff officially live in and is being changed in the wiki, never
to return to the distro?
Any reason those empty dirs aren't nuked out of CVS?
Post by Brian Osborne
Jay, looks like there are still some weird formatting issues with the
bptutorial wiki page, something which I ran into before when getting the
Install docs up for Windows and UNIX (the mediawiki setup thinks 2 or more
spaces preceding a line denotes code for some reason). Not much you can do
in these cases except remove the extra spaces in those spots. Looking good
though!
Sorry, I spent zero time on the whole conversion. I'm not sure what parts
didn't convert well. I've never done that conversion before, and know nothing
about mediawiki. I just blindly let Pod::Simple::Wiki do its thing then ran
off to work. :)
Post by Brian Osborne
I've added a link in the left menu of the wiki. If you think it should
point to the Tutorials page instead of the Bptutorial.pl page please let
me know.
Instead of all these competing links on the left, maybe we should have a
master "documentation" page linked on the left cascading like so?
Documentation (linked on the left menu)
- Quick start
- FAQ
- HOWTOs
- Tutorials
(What's the conceptual difference between a HOWTO and a tutorial?)
It's hard for me to dive into a wiki lifestyle for the huge documentation
pillars since it can't ever get back into the distro... (can it?) Small,
throw away stuff is great for the wiki, but huge, established, thoughtful,
long documents should be left in the distro? Present (and searchable) on the
wiki but static?
Why isn't the short "Current events" just listed on the top of the "News"
page?
Sick of my endless questions yet? -grin-
j
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
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