Hello Lance,
See my inline comments.
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.
The above issues have been corrected in changeset 7621:108cda898646, which is currently available only in the Galaxy central repository. There is a new Galaxy distribution scheduled to go out today, but unfortunately this changeset will not be included. From here on, Galaxy releases are tentatively scheduled for every 2 weeks, so if you don't want to pull from the Galaxy central repository, the fix should be available in the next release 2 weeks from now.
I've slightly altered your tool_dependencies.xml file (mostly because I've implemented support for a new "make_directory" tag. It is attached below - you should updated your tool_dependencies.xml file in your htseq_count repository with this updated version.
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).
Were you attempting to install numpy as another package defined in your tool-dependencies.xml file? If so, the fixes in the above changeset should allow you to do that now since you can install it before htseq and set PYTHONPATH to point to numpy as part of the installation.
Let me know if you need additional help or bump into further problems. The tool dependency installation components are fairly immature, so adding enhancements for new tools like yours is very valuable.
Thanks for your help on this,
Greg Von Kuster
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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