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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