Björn, I have galaxy-dist. Was it the right choice? Here is what I did. I copied your "tool_dependencies.xml" into my project (s_mart, in the test Tool Shed), and I created a testing XML file, which uses your dependencies: --- <tool id="test" name="test"> <description>This is a test.</description> <requirements> <requirement type="set_environment">PYTHONPATH</requirement> <requirement type="set_environment">PATH</requirement> </requirements> <requirement type="package" version="1.7.1">numpy</requirement> <command>env > $outputFile; python -c "import numpy" >> $outputFile</command> <outputs> <data name="outputFile" format="txt" label="output test file"/> </outputs> <help>This is a test.</help> </tool> --- I uninstall and reinstall the package, then run the test. Numpy seems fine (I got no complain), but PYTHONPATH and PATH are not updated. I change "append_to" and "prepend_to" to "set_to" in the "tool_dependencies.xml". I unstall/reinstall my package... the variable dependencies have disappeared! When I run the test, the environment variables are left unchanged. It seems now that Galaxy may have some problems with the reinstall. I tried to totally install my package, but Galaxy remembers having seen it and reinstalls it instead of a fresh install. Could this be the source of the problem? Matthias. On Wed, 24 Apr 2013, Björn Grüning wrote: > Hi Matthias, > >> Sure, >> >> This is the least I can do. However, I do not know how to install a >> package from a simple XML, and without Tool Shed installed repository. > > it's documented here: > http://wiki.galaxyproject.org/Tool% > 20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance > >> I will check that. >> I have downloaded Galaxy for installation less than a week ago. > > Have you downloaded galaxy-dist or galaxy-central? > > Cheers, > Bjoern > >> Matthias. >> >> >> On Wed, 24 Apr 2013, Björn Grüning wrote: >> >>> Hi Matthias, >>> >>> do you use the toolshed or the testtoolshed? >>> Can you please test the following repo and install: >>> >>> testtoolshed.g2.bx.psu.edu/repos/bgruening/package_numpy_1_7 >>> >>> It also contains append_to and works for me. Also which version of >>> galaxy do you use? >>> >>> Thanks! >>> Bjoern >>> >>>> Dear everyone, >>>> >>>> I finally got the answer. The "append_to" does not seem do work in the >>>> "tool_dependencies.xml": >>>> >>>> --- >>>> <environment_variable name="PYTHONPATH" >>>> action="append_to">$REPOSITORY_INSTALL_DIR</environment_variable> >>>> --- >>>> does not insert anything, while: >>>> --- >>>> <environment_variable name="PYTHONPATH" >>>> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> >>>> --- >>>> updates the correct "env.sh" and "INSTALLATION.log" files. >>>> >>>> Weird. >>>> >>>> Many thanks for your help. >>>> >>>> Matthias. >>>> >>>> >>>> On Tue, 23 Apr 2013, Björn Grüning wrote: >>>> >>>>> Hi Matthias, >>>>> >>>>>> Dear Björn, >>>>>> Maybe the problem is here. I cannot find neither "tool_deps", nor >>>>>> "env.sh". >>>>>> The install is fresh from yesterday... I should check why I did not >>>>>> generate these files. >>>>>> By the way, if "env.sh" is sourced right before my script, I should see >>>>>> the updated PYTHONPATH in the result of the command "env > $outputFile", >>>>>> no? >>>>> >>>>> Yes :) >>>>> The tool_deps directory is set in universe_wsgi.ini under: >>>>> tool_dependency_dir = ./tool_deps/ >>>>> >>>>> Ciao, >>>>> Bjoern >>>>> >>>>>> Many thanks, >>>>>> Matthias. >>>>>> >>>>>> >>>>>> On Tue, 23 Apr 2013, Björn Grüning wrote: >>>>>> >>>>>>> Hi Matthias, >>>>>>> >>>>>>> PYTHONPATH will not be changed globally. >>>>>>> It's only changed during execution of your tool. >>>>>>> Have a look under ./tool_deps/.../.../.../s_mart/ there is a file called >>>>>>> env.sh with your PYTHONPATH. >>>>>>> That file is executed before your command >>>>>>> >>>>>>> <command>env > $outputFile</command> >>>>>>> >>>>>>> is executed. >>>>>>> Hope that helps, >>>>>>> Bjoern >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Dear everyone, >>>>>>>> >>>>>>>> I have spent hours trying to set environment variable in Galaxy. I am >>>>>>>> managing the "s_mart" repos (you can check it if you wish), and I created >>>>>>>> the simple files "test.xml" which prints the environment variables: >>>>>>>> --- >>>>>>>> <tool id="test" name="test"> >>>>>>>> <description>This is a test.</description> >>>>>>>> <requirements> >>>>>>>> <requirement type="set_environment">PYTHONPATH</requirement> >>>>>>>> </requirements> >>>>>>>> <command>env > $outputFile</command> >>>>>>>> <outputs> >>>>>>>> <data name="outputFile" format="txt" label="output test >>>>>>>> file"/> >>>>>>>> </outputs> >>>>>>>> <help>This is a test.</help> >>>>>>>> </tool> >>>>>>>> --- >>>>>>>> >>>>>>>> and "tool_dependencies.xml", which appends something to the PYTHONPATH >>>>>>>> variable.: >>>>>>>> --- >>>>>>>> <?xml version="1.0"?> >>>>>>>> <tool_dependency> >>>>>>>> <set_environment version="1.0"> >>>>>>>> <environment_variable name="PYTHONPATH" >>>>>>>> action="append_to">$REPOSITORY_INSTALL_DIR</environment_variable> >>>>>>>> </set_environment> >>>>>>>> </tool_dependency> >>>>>>>> --- >>>>>>>> As you guess, I cannot see anything added in the PYTHONPATH variable. I >>>>>>>> have tried to append INSTALL_DIR and even "/tmp". None worked. >>>>>>>> >>>>>>>> Do you have any suggestion for me? >>>>>>>> >>>>>>>> Many thanks to you all, >>>>>>>> >>>>>>>> Matthias. >>>>>>>> ___________________________________________________________ >>>>>>>> Please keep all replies on the list by using "reply all" >>>>>>>> in your mail client. To manage your subscriptions to this >>>>>>>> and other Galaxy lists, please use the interface at: >>>>>>>> http://lists.bx.psu.edu/ >>>>>>>> >>>>>>>> To search Galaxy mailing lists use the unified search at: >>>>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>>> >>>>>>> >>>>>>> >>>>> >>>>> >>>>> >>> >>> >>> > > -- > Björn Grüning > Albert-Ludwigs-Universität Freiburg > Institute of Pharmaceutical Sciences > Pharmaceutical Bioinformatics > Hermann-Herder-Strasse 9 > D-79104 Freiburg i. Br. > > Tel.: +49 761 203-4872 > Fax.: +49 761 203-97769 > E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de > Web: http://www.pharmaceutical-bioinformatics.org/ > >