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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