I guess this relates directly to my question as well...

On 03/03/2016 01:06 PM, Makis Ladoukakis 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

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Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bakker@wur.nl