Thanks Greg. I used you're updated version and added numpy as a separate dependency. It seems to work in my development system. I haven't updated my qa or production versions yet, so I can't check there. Perhaps you could test it and let me know if there are issues, etc.

Glad I can be of help.

Lance

Greg Von Kuster wrote:
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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--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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