Problem using FastQC in Galaxy
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.bioinformatics@gmail.com <contato@gilsonleite.com.br>
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? -Dannon 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?
Thanks
--
*Alfredo Guilherme da Silva Souza* Distributed Systems and Computer Networks Federal University of São Carlos - UFSCar Contact +55 16 9115-3035 | alfredo.bioinformatics@gmail.com <contato@gilsonleite.com.br>
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Hi, why do you need biopython for FASTQC? You can install biopython from the ToolShed and can depend on it: https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_64 Cheers, Bjoern Am 05.01.2015 um 19:01 schrieb 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>* * 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
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Thanks :) 2015-01-05 16:45 GMT-02:00 Björn Grüning <bjoern.gruening@gmail.com>:
Hi,
why do you need biopython for FASTQC? You can install biopython from the ToolShed and can depend on it:
https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_64
Cheers, Bjoern
Has anyone used the Biopython in Galaxy ?
*Traceback (most recent call last):* * File "/home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py",
Am 05.01.2015 um 19:01 schrieb Alfredo Guilherme Silva Souza: 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
___________________________________________________________ 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/
-- *Alfredo Guilherme da Silva Souza* Distributed Systems and Computer Networks Federal University of São Carlos - UFSCar Contact +55 16 9115-3035 | alfredo.bioinformatics@gmail.com <contato@gilsonleite.com.br>
participants (3)
-
Alfredo Guilherme Silva Souza -
Björn Grüning -
Dannon Baker