[Bioperl-l] removing BioPerl 1.x from CPAN ?

Fri Jan 21 18:27:12 UTC 2011

Ben,

No, BioPerl and BioPerl-Run are two separate distributions or packages:

http://www.bioperl.org/wiki/Category:BioPerl_Packages

A good number of Bio::DB::* modules on CPAN are currently part of BioPerl (also known as the core modules; 'bioperl-live' are the bleeding edge modules found on github).  A number, like Bio::DB::Sam, are found in other distributions (Lincoln's Bio-Samtools).  The code you need is in BioPerl itself, and was added by Mark Jensen after the 1.6.1 release.  If you use the CPAN shell and use 'm /Bio::DB/', you will see a list of the modules and the associated distributions they belong to.

Final note: Dist::Zilla isn't required reading for anyone using BioPerl code, only those who may want to act as release managers in the future (for BioPerl or any other Perl project).  It's merely a nice tool that dramatically simplifies:

1) Updating changes
2) Changing the version
3) Testing the code
4) Packaging up the code for CPAN
5) Uploading to CPAN for others to enjoy

I mention it here for those who use github, as many Dist::Zilla conversions lack a Makefile.PL/Build.PL.  We would have to retain one for many reasons too involved to talk about here.

chris

On Jan 21, 2011, at 9:55 AM, Ben Bimber wrote:

> Hi Chris,
> 
> Perhaps there is some subtle difference I'm not catching.  I thought
> that 'BioPerl' referred collectively to bioperl-live and bioperl-run.
> There are also a number of other 'Bio::XX' packages out there that are
> not BioPerl, like Bio::DB.  The specific bugfix I need is in
> CommandExts.pm, which is part of the wrapper code in the bioperl-run
> repository.
> 
> I have only 2 servers to keep track of, so downloading from GIT was
> honestly just simpler and faster than figuring out a proper solution.
> I will do some reading on Dist::Zilla.
> 
> -Ben
> 
> 
> 
> On Fri, Jan 21, 2011 at 9:49 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> Do you need updates to bioperl, or to bioperl-run?  The reason I ask is one of the things I really want to push towards is using Dist::Zilla for us developers who want an easier way to make releases, with a default Build.PL so one doesn't have to install Dist::Zilla to use the latest code.  bioperl-run might be a good place to test this out.
>> 
>> chris
>> 
>> On Jan 21, 2011, at 9:41 AM, Ben Bimber wrote:
>> 
>>> I also have no problem removing the old version.  All the different
>>> BioPerl variants made it difficult to install the right version back
>>> when I first did it.
>>> 
>>> I'd love even more if the version on CPAN was updated though.  I'd
>>> been using a copy from GIT for a while b/c I need changes made to the
>>> bioperl-run wrapper code.
>>> 
>>> -Ben
>>> 
>>> 
>>>>> Message: 2
>>>>> Date: Thu, 20 Jan 2011 17:11:01 +0100
>>>>> From: Dave Messina <David.Messina at sbc.su.se>
>>>>> Subject: [Bioperl-l] removing BioPerl 1.x from CPAN ? request for
>>>>>       comment
>>>>> To: Dave Messina <David.Messina at sbc.su.se>
>>>>> Message-ID: <F4E417F1-6D80-4C70-ADEE-B25AB291E730 at sbc.su.se>
>>>>> Content-Type: text/plain; charset=us-ascii
>>>>> 
>>>>> Hi everybody,
>>>>> 
>>>>> As some of you have no doubt noticed, we have a persistent problem with users accidentally using BioPerl versions 1.4 and earlier. Although they've been placed on BackPAN, CPAN's archive for deprecated software, for some reason they still show up in CPAN search results.
>>>>> 
>>>>> It's frustrating for users to be directed to the wrong version of the software, adding another gotcha to an already too-complicated installation process. And to this day it generates support emails on this list.
>>>>> 
>>>>> As far as I know, the Ensembl Perl API still designates version 1.2.3 of BioPerl for use with it:
>>>>> 
>>>>>       http://www.ensembl.org/info/docs/api/api_installation.html
>>>>> 
>>>>> (although in Chris Fields' testing, the Ensembl API worked just fine with the current BioPerl version, 1.6.x.)
>>>>> 
>>>>> 
>>>>> I intend to ask the CPAN admins to remove BioPerl 1.4 and earlier entirely. But before I do, I wanted to raise the issue here in case anyone objects. In particular, it'd be great if someone from Ensembl could weigh in on this. I should also point out that we have these earlier releases archived on github already, so they will still be available.
>>>>> 
>>>>> 
>>>>> Thanks,
>>>>> Dave
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> ------------------------------
>>>>> 
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>>>>> Bioperl-l at lists.open-bio.org
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>>>>> 
>>>>> End of Bioperl-l Digest, Vol 93, Issue 16
>>>>> *****************************************
>>>> 
>>>> --
>>>> William Spooner
>>>> whs at eaglegenomics.com
>>>> http://www.eaglegenomics.com
>>>> 
>>>> 
>>>> 
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