I modified the PYTHONPATH in htseq_count (http://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) and cutadapt (http://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt). It would be great to have some common dependencies setup in the toolshed such as numpy, etc.

Lance

Björn Grüning wrote:
Hi Peter,

On Wed, Apr 17, 2013 at 6:05 PM, James Taylor<ja...@jamestaylor.org>  wrote:
No it does not have root, and it is very important that we not install
anything at the system level since we need to maintain version
isolation. We should always be able to inject things into the
environment so that Python/Perl/R look in the right place.
So is there any guidance on how that is best done?

I do not now it it is best practise but have a look at

package_numpy_1_7 and
package_matplotlib_1_2

I will try to setup a few common python deps, so we can include them
easily in tool_dependecies.xml

Python has various options including virtual env, but I
doubt we can make any assumptions about the host
system's python - even which version exactly. Does
that mean installing Python modules locally and then
manipulating the PYTHONPATH is the best plan?

Thanks,

Peter
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--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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