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Some of the scripts linked here are not found #61

Open cjfields opened 8 years ago

cjfields commented 8 years ago

Author Name: Bernd empty (Bernd empty) Original Redmine Issue: 2912, https://redmine.open-bio.org/issues/2912 Original Date: 2009-09-09 Original Assignee: Bioperl Guts

The bioperl scripts section at http://www.bioperl.org/wiki/Bioperl\_scripts is really handy for short examples. However, it quite a number of scripts cannot be found anymore and return errors:

For example for the first link (scripts/install_bioperl_scripts.pl) Filesystem has no item: File not found: revision 15800, path ‘/bioperl-live/trunk/scripts/install_bioperl_scripts.pl’ at /usr/lib/perl5/site_perl/5.8.8/SVN/Web/action.pm line 245

Also “no item” for e.g. http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/scripts/Bio-DB-GFF/pg\_bulk\_load\_gff.PLS

Possible the Bio::Graphics example scripts could be linked to the new Bio::Graphics repo? The examples are quite informative.

Cheers, Bernd

cjfields commented 8 years ago

Original Redmine Comment Author Name: Mauricio Herrera Original Date: 2010-05-13T14:38:22Z

Hi Bernd,

Can you take care of updating such wiki page to list only the existing scripts? Also, can you update each of the links to point to their new github locations?

Thanks, Mauricio.

cjfields commented 8 years ago

Original Redmine Comment Author Name: Bernd empty Original Date: 2010-05-13T15:09:41Z

Hi Mauricio,

I can change the links to Git, i will create an bioperl.org WIKI account. However, one issue remains: the Bio::Graphics scripts in 1.5.2 (both example/ and scipts/) have disappeared from the repo as Bio::Graphics was removed. Can we somehow re-add these scripts to the new bioperl-live? Otherwise I am not sure how to link to them (i’d rather not link out to a third server)

Bernd

cjfields commented 8 years ago

Original Redmine Comment Author Name: Mauricio Herrera Original Date: 2010-05-13T15:16:04Z

I believe that should be discussed at the bioperl-l mailing list, as the Bio::Graphics removal had a purpose. I don’t think the core devs would want to re-add it to the bioperl-live repository. Maybe Chris can propose a solution?

(In reply to comment #2)

Hi Mauricio,

I can change the links to Git, i will create an bioperl.org WIKI account. However, one issue remains: the Bio::Graphics scripts in 1.5.2 (both example/ and scipts/) have disappeared from the repo as Bio::Graphics was removed. Can we somehow re-add these scripts to the new bioperl-live? Otherwise I am not sure how to link to them (i’d rather not link out to a third server)

Bernd

cjfields commented 8 years ago

Original Redmine Comment Author Name: Dave Messina Original Date: 2010-05-13T15:36:14Z

As far as I can tell, the scripts are still distributed with Bio::Graphics, which is a separate distibution now on CPAN.

How about we just put a link to the Bio-Graphics package? Such as:

http://search.cpan.org/search?query=Bio%3A%3Agraphics&mode=all

which should always find the latest version.

Dave

cjfields commented 8 years ago

Original Redmine Comment Author Name: Chris Fields Original Date: 2010-05-13T15:52:08Z

(In reply to comment #4)

As far as I can tell, the scripts are still distributed with Bio::Graphics, which is a separate distibution now on CPAN.

How about we just put a link to the Bio-Graphics package? Such as:

http://search.cpan.org/search?query=Bio%3A%3Agraphics&mode=all

which should always find the latest version.

Dave

Might be best to have this page autogenerated somehow, opposed to having to revise it every time we have a change to bioperl-live. So maybe a longer term solution is to come up with a script that just generates the wiki text every so often, then updates it?

cjfields commented 8 years ago

Original Redmine Comment Author Name: Mauricio Herrera Original Date: 2010-05-13T15:55:58Z

That sounds great. Anyone up for trying it?

(In reply to comment #5)

Might be best to have this page autogenerated somehow, opposed to having to revise it every time we have a change to bioperl-live. So maybe a longer term solution is to come up with a script that just generates the wiki text every so often, then updates it?

cjfields commented 8 years ago

Original Redmine Comment Author Name: Chris Fields Original Date: 2010-05-13T17:41:50Z

Could parse the scripts for summary info, and use something like:

http://search.cpan.org/perldoc?MediaWiki::API

chris

(In reply to comment #6)

That sounds great. Anyone up for trying it?

(In reply to comment #5)

Might be best to have this page autogenerated somehow, opposed to having to revise it every time we have a change to bioperl-live. So maybe a longer term solution is to come up with a script that just generates the wiki text every so often, then updates it?

cjfields commented 8 years ago

Original Redmine Comment Author Name: Mauricio Herrera Original Date: 2010-05-20T16:11:21Z

Wiki template has been updated to point to the new Github repository. We still need a solution to autorefresh the list of scripts in this page.

(In reply to comment #7)

Could parse the scripts for summary info, and use something like:

http://search.cpan.org/perldoc?MediaWiki::API

chris

(In reply to comment #6)

That sounds great. Anyone up for trying it?

(In reply to comment #5)

Might be best to have this page autogenerated somehow, opposed to having to revise it every time we have a change to bioperl-live. So maybe a longer term solution is to come up with a script that just generates the wiki text every so often, then updates it?