Hey Alfredo,

You shouldn't have to mess with eggs for tools -- those are primarily dependencies of the core framework itself.  Do you have biopython installed and available in the environment (PYTHONPATH) of whatever user jobs are run as?  That is, if you open a plain python shell as the galaxy user, does that import work?


On Mon, Jan 5, 2015 at 1:01 PM, Alfredo Guilherme Silva Souza <alfredo.bioinformatics@gmail.com> wrote:

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>
    import Bio.PDB.PDBParser
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

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