Yeah Linda, this was the case for me. When I started the virtual environment I
reinstalled BioPython and everything worked again. I suggest you do the same to
any packages you need for your tools.
Makis
To: galaxy-dev@lists.galaxyproject.org
From: linda.bak...@wur.nl
Date: Thu, 3 Mar 2016 14:10:44 +0100
Subject: Re: [galaxy-dev] Python script can't can't import BioPython modules in
Galaxy 16.01
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.bak...@wur.nl
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___________________________________________________________
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