Looks like it's working! The problem I had run into, in hindsight, was a) I hadn't set tool_dependency_dir as I didn't know about it b) if I had set it, I was installing tools to $SW/tool-name/version-number/ but the default tool wrappers in galaxy-dist don't have version numbers set, so they will just look in $SW/tool-name/ . Can I suggest this be added to the wiki somewhere under the Admin pages? Apologies if it's there, I couldn't find it except under News Briefs at http://wiki.g2.bx.psu.edu/News%20Briefs/2010_11_24?highlight=%28tool_depende... . As well as being on the wiki it would be useful to have it (commented out by default) in universe_wsgi.ini. I think the tool_dependency_dir variable isn't in there at all at the moment, at least in the galaxy-dist I have. It would also be useful to have a brief mention or link to it on http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup to save time for people like me who had tools installed in a non-standard place. Thanks again! Clare On Wed, Nov 16, 2011 at 3:01 PM, Clare Sloggett <sloc@unimelb.edu.au> wrote:
Great! Thanks James, this is exactly what I need.
On Wed, Nov 16, 2011 at 2:20 PM, James Taylor <james@jamestaylor.org> wrote:
On Nov 15, 2011, at 9:59 PM, Clare Sloggett wrote:
If this is the case, what is the best way to install and maintain two versions of the same tool? I can write code into the wrapper to find the correct version of the tool in a given case, but I was wondering if there is a more standard 'galaxy' way to configure this.
You should provide "tool_dependency_dir" in the config file and point it at some directory $SW where you will install tools under.
With this enabled, when a tool has a dependency, Galaxy will look for it under that directory and attempt to run a script to setup the environment. For example if you have tool with a dependency on foo version 1.3, Galaxy will look for:
$SW/foo/1.3/env.sh
and if found will source it as part of the job submission script. This usually contains something simple like
PATH=$PACKAGE_BASE/bin:$PATH
to add the binaries installed with the dependency to the path.
Ideally all dependencies used by Galaxy tools would be installed in this way.
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759
-- E: sloc@unimelb.edu.au P: 03 903 53357 M: 0414 854 759