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.
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/
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? 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/
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/
Many thanks! However, how matter how hard I try, I cannot see anything in this directory. I will investigate that. À bientôt, 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/
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/
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/
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. I will check that. I have downloaded Galaxy for installation less than a week ago. 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/
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/
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/
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.
Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/
Dear Björn, Is not it what I did? I wrote "<requirement type="package" version="1.7.1">numpy</requirement>" in "test.xml", and the version number is the same as yours... Many thanks again, Matthias. On Thu, 25 Apr 2013, Björn Grüning wrote:
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.
Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/
Hello everyone, I would like to automagically install an R package when installing my tool. So I wrote this in my "tool_dependencies.xml": --- <package name="R_PACKAGES" version="1.0"> <install version="1.0"> <actions> <action type="shell_command">R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in% rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'</action> </actions> </install> </package> --- This does not seem to work and the problem is: --- /bin/sh: 1: cd: can't cd to ./database/tmp/tmpI6RcEu/R_PACKAGES --- What is true is that I have this in the Galaxy log: --- Warning: local() encountered an error (return code 2) while executing 'R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in% rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'' [localhost] local: rm -rf ./database/tmp/tmpI6RcEu --- I do not think that the local error is related (I have it everywhere), but a premature "rm -rf ./database/tmp/tmpI6RcEu" might explain the problem. I tried another install (e.g. package_samtools_0_1_16), which downloads and makes the samtools: no problem. Does anyone have a suggestion? Many thanks, Matthias.
participants (2)
-
Björn Grüning -
Matthias Zytnicki