Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01
On Thu, Mar 3, 2016 at 12:06 PM, Makis Ladoukakis
<makis4ever(a)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.
Peter