biopython installation

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biopython installation

Lapointe, David
I tried installing biopython and dependancies from the toolshed but this does not seem to be functional even though these tools say INSTALLED.  Is there something that I should do that I missed?  I sis better to installed them in the regular python fashion?
-- 
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research and Geospatial Technology Services
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144

Phone:  617-627-5319
Fax: 617-627-3667
http://it.tufts.edu

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Re: biopython installation

Peter Cock
On Fri, Feb 20, 2015 at 3:56 PM, Lapointe, David
<[hidden email]> wrote:
> I tried installing biopython and dependancies from the toolshed but this
> does not seem to be functional even though these tools say INSTALLED.

How are you testing it? Any Galaxy copy of Biopython will not be
available to the system Python.

> Is there something that I should do that I missed?  I sis better to installed
> them in the regular python fashion?

Any Galaxy tool which wants access to a Galaxy copy of Biopython
needs to declare this as an explicit dependency.

e.g. http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss

Peter
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