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.fernan...@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.sora...@gmail.com] On Behalf Of Nicola
> Soranzo
> Sent: October-07-16 3:14 PM
> To: Fernandez Edgar <edgar.fernan...@umontreal.ca>; galaxy-...@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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