Are you writing your own tool, or trying to install someone else's?
There are two basic options,
(1) Install Biopython into the default Python used when jobs are
run. Simple, but manual - and you can only have one version.
This is actually what we are still doing on our local Galaxy
since we started before the second option as available.
(2) Install Biopython via the ToolShed, using the dependency
mechanism. This allows multiple versions of Biopython (or any
Python library) to be installed in parallel, and Galaxy does the
setup to ensure the declared dependency is on the Python
path when your script is run. e.g.
declares a dependency on:
(which in turn depends on NumPy etc).
This reminds me, we are overdue to create a Galaxy ToolShed
package for Biopython 1.65, I must do that...
On Mon, Jan 5, 2015 at 6:16 PM, Alfredo Guilherme Silva Souza
Has anyone used the Biopython in Galaxy ?
Traceback (most recent call last):
File "/home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py", line
10, in <module>
ImportError: No module named Bio.PDB.PDBParser
Researching I saw that I have to work with eggs in the Galaxy. Has anyone
done this with Biopython? Is it really necessary?
Alfredo Guilherme da Silva Souza
Distributed Systems and Computer Networks
Federal University of São Carlos - UFSCar
Contact +55 16 9115-3035 | alfredo.bioinformatics(a)gmail.com
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