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abims-sbr / galaxy-blastvisu

Visualisation for Blast XML outputs under Galaxy
http://abims.sb-roscoff.fr/
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Blastvisu need Biopython #2

Open lecorguille opened 8 years ago

lecorguille commented 8 years ago

During Emma intership, the visualisation was a tool and works well. During Caroline intership, the visualisation become a real visualisation and work well on her setup.

But on a production Galaxy instance, Biopython is needed but seems not available

Module blastvisu_mako:68 in render_body         view
>>  from Bio.Blast import NCBIXML
ImportError: No module named Bio.Blast

So, we will need to find a way:

bgruening commented 8 years ago

I guess you need to have this installed into the Galaxy venv to make it work. @guerler is it possible to have a requirement tag inside the visualisation.xml file? This way we could hook up arbitrary dependencies in visualisations.

lecorguille commented 8 years ago

Indeed, my next move will be to install Biopython in the Venv. But I was surprise because the user galaxy can access to the lib Biopython installed on the cluster. I haven't search so much.

And sure, it would be great if there is a system of tool dependenties.