This is an annoyance from the NCBI team, and dealing with the expired tbl2asn tool is a regular question from Prokka users, eg: https://github.com/tseemann/prokka/issues/96 https://github.com/tseemann/prokka/issues/139 The Tool Shed package for Prokka will need updating - but luckily Nicola is already working on that: https://github.com/galaxyproject/tools-iuc/pull/985 I'm not sure if this will work, but you can try manually installing the latest tbl2asn from the NCBI (and if need be, copy the binary on top of the expired binary from the Tool Shed - messy!): ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/ Peter On Tue, Oct 18, 2016 at 7:19 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca> wrote:

Hey Guys,

I’ve fixed this problem by bypassing the system perl and compiling my own with all the right modules.

So I don’t get any more perl errors.

Also, I’ve realized that the latest prokka package (Revision: f5e44aad6498) has a dependency with the package_tbl2_asn_24_3 (Revision 41764d6a6a3c).

However, when you execute prokka, tbl2asn gives you the following error:

[tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version.

What would you suggest I do?

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

From: Nicola Soranzo [mailto:nicola.soranzo@gmail.com] On Behalf Of Nicola Soranzo Sent: October-07-16 3:14 PM To: Fernandez Edgar <edgar.fernandez@umontreal.ca>; galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] galaxy - bioperl - prokka

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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