Installing dependencies from toolshed fails and produces strange folder
Hi all, Updating our Galaxy: the migration of some tools to the toolshed (let's take picard as an example) and installing them back from the toolshed worked well. However, during the update, I forgot to install the dependencies. So I went to the administration part of our Galaxy, and selected 'Manage installed tool shed repositories <http://galaxy.bits.vib.be/admin_toolshed/browse_repositories>'. With the interface, I installed the dependencies for the tool (*Tool shed repository 'picard' tool dependencies*): but this failed with an error (SystemError: 1 or something alike). After this error, I noticed a strange folder was created in the Galaxy root called '. Meaning, really called ', like "'" :-) $GALAXY_HOME/'/apps'/picard/1.56.0/devteam/picard/<revisionid>/jars The installer installed all jars in this folder. I am currently looking into the code, but my first reflex was to think: the path is not correctly set, so heading to universe_wsgi.ini! But this seemed to be a wrong guess. Any idea what parameters are wrongly set here? Cheers and thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
Hello Joachim, Tool dependencies are installed into the location defined by the following entry in your universe_wsgi.ini file. # Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies tool_dependency_dir = ../tool_dependencies Greg Von Kuster On Jan 8, 2013, at 10:45 AM, Joachim Jacob wrote:
Hi all,
Updating our Galaxy: the migration of some tools to the toolshed (let's take picard as an example) and installing them back from the toolshed worked well. However, during the update, I forgot to install the dependencies.
So I went to the administration part of our Galaxy, and selected 'Manage installed tool shed repositories <http://galaxy.bits.vib.be/admin_toolshed/browse_repositories>'. With the interface, I installed the dependencies for the tool (*Tool shed repository 'picard' tool dependencies*): but this failed with an error (SystemError: 1 or something alike).
After this error, I noticed a strange folder was created in the Galaxy root called '. Meaning, really called ', like "'" :-) $GALAXY_HOME/'/apps'/picard/1.56.0/devteam/picard/<revisionid>/jars
The installer installed all jars in this folder. I am currently looking into the code, but my first reflex was to think: the path is not correctly set, so heading to universe_wsgi.ini! But this seemed to be a wrong guess. Any idea what parameters are wrongly set here?
Cheers and thanks, Joachim
-- Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
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participants (2)
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Greg Von Kuster -
Joachim Jacob