Problem with custom tool that uses bioperl modules in local Galaxy instance

Question: Problem with custom tool that uses bioperl modules in local Galaxy instance

18 months ago by

Hello,

I am writing custom tool for Galaxy that uses perl scripts and bioperl modules. My instance recognize the tool but when try to use it I get the following error :

Fatal error: Exit code 2 () Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: ~/galaxy/tools/ExSpOD/modules /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /home/cidam/galaxy/tools/ExSpOD/ExSpOD.pl line 23. BEGIN failed--compilation aborted at /home/cidam/galaxy/tools/ExSpOD/ExSpOD.pl line 23.

But in the "~/galaxy/tools/ExSpOD/modules" there all the needed bioperl modules. My script uses the following line to indicate where to find the modules (aka "~/galaxy/tools/ExSpOD/modules") :

use lib "$ENV{PWD}/modules";

I don't understand where is the problem. Maybe should I use another method to indicate the module library ? Or find a way to install the bioperl modules in Galaxy ?

Thank you.

bioperl galaxy custom perl • 726 views

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modified 18 months ago by Dave B. ♦ 410 • written 18 months ago by martin.pettinotti • 10

18 months ago by

Dave B. ♦ 410

United States

Dave B. ♦ 410 wrote:

Hello,

That method of providing tool dependencies is not really recommended. It would be more robust to specify a dependency on the perl-bioperl package, like so:

<requirement type="package" version="1.6.924">perl-bioperl</requirement>

And then configure your galaxy instance to install and resolve conda dependencies as described in this FAQ:

https://docs.galaxyproject.org/en/master/admin/conda_faq.html

The first time you run ExSpOD after making those changes, it will install bioperl and all its requirements into an environment in which the tool will then run.

ADD COMMENT • link written 18 months ago by Dave B. ♦ 410

Thanks, the problem is resolved now.

ADD REPLY • link written 18 months ago by martin.pettinotti • 10

Hi, I have a local instance of galaxy and have a tool written in Perl using some module . I have the same problem as you however i put the requirement tag in my xml file and the dependencies is successfully installed .

ADD REPLY • link written 5 months ago by Justine.POLLET • 0

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