Hi Matthias, you need to add something like the following to your tool defintion: <requirements> <requirement type="package" version="1.1p1">chemfp</requirement> </requirements> The version and the name needs to be the same as in your tool_dependency.xml. Cheers, Bjoern
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.
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