On Thu, Mar 3, 2016 at 12:06 PM, Makis Ladoukakis
<makis4e...@hotmail.com> wrote:
> Hello everyone,
> I've recently upgraded to Galaxy 16.01 and i have some issues with a python
> wrapper from a tool. When I run it via Galaxy I get the following error:
> Traceback (most recent call last):
>   File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py",
> line 12, in <module>
>     from Bio import SeqIO
> ImportError: No module named Bio
> However when I click on the "view details" icon to copy the command from the
> tool and run it on my command line the tool works perfectly. In addition
> this issue occurs while I already have installed BioPython.
> When I type Python and write  "from Bio import SeqIO" I get no error.
> Can this be an issue related to the virtual environment that is initialized
> each time Galaxy starts?
> Thank you in advance,
> Makis Ladoukakis

Almost certainly, yes, this is due to the new venv setup in Galaxy.

If you had manually installed Biopython, I would suggest you install it
again but inside the venv.

If you installed Biopython via the Tool Shed package, that is more troubling.
Try doing a re-install via the Tool Shed.

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