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
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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Greg Von Kuster -
Joachim Jacob