I've put together a tool wrapper for the htseq-count script that is part of the HTSeq python package and uploaded that to the tool shed. However, I have discovered that the tool dependancies do not install properly. There are a couple of issues that I've run into.

1) The biggest issue is the inability to set both the PYTHONPATH and PATH environment variables as part of installation. If I put two separate <action type="set_environment"> tags, then the second overwrites the first in the env.sh file. If instead, I put two <environment_variable> tags within the action, only one (the second) gets executed during installation.


2) Another issue is the inability to install Numpy as a dependancy to HTSeq. I can get Numpy to install, but it won't be in the PYTHONPATH when HTSeq is installed (or executed).

Any thoughts on how to address these issues would be appreciated.

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

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