Florent, maybe your questions better reside in the dev-list but anyway we have encounter similar things for various reasons. When plugging binaries/tools outside galaxy it works setting paths and such.... but PATH environments and other ENVironmental variables are usually not directly set for the running galaxy user (since it phusically doesn't get into shell. We therefore source the /etc/profile in the galaxy server startup script to be sure to have the correct environmentals set as is for the other users. What I do not understand is that the tools seem to work when logged in fysically as galaxy user....in our case the tools wouldn't have worked. Are you sure (I think you are but you never know) that its a perl script? Ocassionally we have seen something like this but was solved by omitting the interpreter part in the tool config xml or setting it to bash. Good luck. Alex ________________________________________ Van: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] namens Florent Angly [florent.angly@gmail.com] Verzonden: zondag 13 februari 2011 9:03 Aan: galaxy-user@lists.bx.psu.edu Onderwerp: [galaxy-user] Galaxy does not find my executables 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 Usage: Grinder [options] Grinder --help Grinder --version ... Grinder's location is: $ which Grinder /opt/local/bin/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: PERL=/usr/bin/perl PATH=/usr/bin:/bin:/usr/sbin:/sbin While on the command line, the environment is: PERL=/opt/local/bin/perl PATH=/opt/local/bin:/opt/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/sw/bin 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, Florent _______________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/