Yes ;) 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. https://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss declares a dependency on: https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_62 (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... Regards, Peter On Mon, Jan 5, 2015 at 6:16 PM, Alfredo Guilherme Silva Souza <alfredo.bioinformat...@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? > > > Thanks > > > > > -- > > Alfredo Guilherme da Silva Souza > Distributed Systems and Computer Networks > Federal University of São Carlos - UFSCar > Contact +55 16 9115-3035 | alfredo.bioinformat...@gmail.com > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
