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/