Hi list,

I am writing a wrapper for a Grinder, a Perl program installed globally on my Galaxy server.

Galaxy runs as user 'galaxy':
$ ps aux | grep paster
galaxy 26807 0.0 0.8 2636308 136364 ?? S 2:52PM 0:19.15 python ./scripts/paster.py serve universe_wsgi.ini

When logged in as user galaxy, I can run Grinder:
$ Grinder --help
           Grinder [options]
           Grinder --help
           Grinder --version

Grinder's location is:
$ which Grinder

In grinder.xml:
If I put: <command interpreter="perl">
In the Galaxy webinterface, I get the error: Can't open perl script "/Users/galaxy/galaxy_dist/tools/ngs_simulation/Grinder": No such file or directory Obviously, here, Galaxy assumes wrongly that tool is installed under the Galaxy ~/tools/ngs_simulation/ folder.

So I tried to omit the interpreter: <command>
And I got the error: /bin/sh: Grinder: command not found
This is surprising, since Grinder is found if I run it on the command-line as user galaxy

I noticed that I have the same issue with the Velvet wrapper (also located in /opt/local/bin) and thought that this could be an environment issue. And indeed the environment within a wrapper is:

While on the command line, the environment is:

This difference in environment explains why Galaxy cannot find Grinder or Velvet.

Does this make any sense? Does Galaxy modify the environment? Why would the environment be different?

Thanks for your help,


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