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//*
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/