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/