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 > > ___________________________________________________________ > 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/
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