Problem using FastQC in Galaxy

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Problem using FastQC in Galaxy

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


--

Alfredo Guilherme da Silva Souza
Distributed Systems and Computer Networks
Federal University of São Carlos - UFSCar



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Re: Problem using FastQC in Galaxy

Dannon Baker-2
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 <[hidden email]> 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



___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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  http://galaxyproject.org/search/mailinglists/


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Re: Problem using FastQC in Galaxy

Björn Grüning-3
In reply to this post by Alfredo Guilherme Silva Souza
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
>
>
>
>
> ___________________________________________________________
> 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:
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Re: Problem using FastQC in Galaxy

Alfredo Guilherme Silva Souza

Thanks :)

2015-01-05 16:45 GMT-02:00 Björn Grüning <[hidden email]>:
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
>
>
>
>
> ___________________________________________________________
> 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



___________________________________________________________
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/