Hi Lance,

I installed your htseq repository and all 3 tool dependencies installed fine on 
my mac, so the xml definition works!

Greg Von Kuster

On Sep 11, 2012, at 5:50 PM, Lance Parsons wrote:

> 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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