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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