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<james@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 ___________________________________________________________ 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: http://lists.bx.psu.edu/
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___________________________________________________________ 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: http://lists.bx.psu.edu/
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-- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University