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.

Attachment: tool_dependencies.xml
Description: XML document



> 
> 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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