Question: Problem with custom tool that uses bioperl modules in local Galaxy instance
0
gravatar for martin.pettinotti
4 months ago by
martin.pettinotti0 wrote:

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 • 171 views
ADD COMMENTlink modified 4 months ago by Dave B.410 • written 4 months ago by martin.pettinotti0
1
gravatar for Dave B.
4 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 COMMENTlink written 4 months ago by Dave B.410

Thanks, the problem is resolved now.

ADD REPLYlink written 4 months ago by martin.pettinotti0
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