Hi Lance, Thanks for reporting these issues - the tool dependencies component is fairly new, so you may have uncovered some problems that need correction. I'll take a look at these. make corrections if necessary, and get back to you when all is functional. Thanks! Greg Von Kuster On Sep 4, 2012, at 3:15 PM, Lance Parsons wrote:
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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