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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