Thanks Dave, for letting me see the more useful stuff you can do with env.sh. Unfortunately, env.sh is not available in that tool_dependency_dir after installing the dependencies. I had my path set between quotes in the universe_wsgi.ini, producing unwanted results (the ' folder). (fe, tool_dependency_dir = '/apps'). Hence, the dependencies were installed in a place I did not want to - I moved them to the right path. BUT, no env.sh is in that folder. I cannot reinstall the dependencies via the interface neither. The quick fix I want to avoid, setting all paths hardcoded in picard tools :-/ [galaxy@galaxy e0232cbac965]$ pwd /apps/picard/1.56.0/devteam/picard/e0232cbac965 [galaxy@galaxy e0232cbac965]$ ll -alh total 12K drwxrwxr-x 3 galaxy galaxy 4.0K Jan 8 15:07 . drwxrwxr-x 3 galaxy galaxy 4.0K Jan 8 15:07 .. drwxrwxr-x 2 galaxy galaxy 4.0K Jan 8 15:07 jars I created a simple env.sh myself in that folder, but no avail. #!/bin/bash JAVA_JAR_PATH=`pwd`/jars Small question: should there not be included in the tool's xml file a statement: <requirement type="set_environment">JAVA_JAR_PATH</requirement> See http://wiki.galaxyproject.org/ToolShedToolFeatures?highlight=%28env.sh%29 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 On 01/08/2013 05:53 PM, Dave Bouvier wrote:
Joachim,
JAVA_JAR_PATH is set in env.sh, which is generated during the tool dependency installation process and saved to <tool_dependency_dir>/picard/1.56.0/devteam/picard/<revisionid>/env.sh
The install code sets this variable to <tool_dependency_dir>/picard/1.56.0/devteam/picard/<revisionid>/jars
--Dave B.
*From: *Joachim Jacob <joachim.jacob@vib.be <mailto:joachim.jacob@vib.be>> *Date: *January 8, 2013 11:06:17 AM EST *To: *Greg Von Kuster <greg@bx.psu.edu <mailto:greg@bx.psu.edu>> *Subject: **Re: [galaxy-dev] Installing dependencies from toolshed fails and produces strange folder* *Reply-To: *joachim.jacob@vib.be <mailto:joachim.jacob@vib.be>
Thanks. And where is the JAVA_JAR_PATH set?
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib
On 01/08/2013 04:55 PM, Greg Von Kuster wrote:
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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