Hi Edgar,
presently the Prokka wrapper requires some dependencies (in particular some Perl modules) to be installed separetely, see the README file at https://toolshed.g2.bx.psu.edu/view/crs4/prokka/


We are planning to release an updated Prokka wrapper which will use Conda dependencies, you can track the progress at:

https://github.com/galaxyproject/tools-iuc/pull/985

Cheers,
Nicola

On 07/10/16 15:06, Fernandez Edgar wrote:

Hello,

I have installed prokka, perl and bioperl in my Galaxy’s ToolShed.

However, my users are getting this error during execution of prokka:

Can't locate Bio/Root/Version.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/prokka/1.11/crs4/prokka/f5e44aad6498/bin/prokka line 29. BEGIN failed--compilation aborted at /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/prokka/1.11/crs4/prokka/f5e44aad6498/bin/prokka line 29.

I was under the impression that the galaxy’s tools will use the internal perl.

Do I just need to install Bio::Root:Version on my system installation of perl?

Please give me whatever information you can on this issue.

Regards,

*Edgar Fernandez*

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication*//*

*/Université de Montréal/*

*//*

PAVILLON ROGER-GAUDRY, bureau X-210

(Bur. : *1-514-343-6111 poste 16568//*



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