Problem with Biopython

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Problem with Biopython

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 with Biopython

Peter Cock
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
<[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
> Contact +55 16 9115-3035 | [hidden email]
>
>
>
> ___________________________________________________________
> 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/
___________________________________________________________
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Re: Problem with Biopython

Peter Cock
On Tue, Jan 6, 2015 at 12:23 AM, Peter Cock <[hidden email]> wrote:

> 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...

Done,
https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_65

And for tool developers on the TestToolShed too,
https://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_65

Peter
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