Instead of modifying the environment variables directly, I've found it easier
to use Galaxy's built in tool dependency framework. All you'd have to do is
add a <requirements type="package"> tag to your custom tools to specify the
package directory that needs to be checked at runtime.
See http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies, specifically
the "Managed Tool Dependencies" section. Many of the other tools on the cloud
volume use the 'env.sh' method discussed there. For example, blast has the
'blast' package requirement, and in the /mnt/galaxyTools/blast/default
directory you'll find an 'env.sh' file that configures the environment at
On Jun 13, 2012, at 8:49 PM, Jose Navas wrote:
> Hi Galaxy Team,
> I'm modifying my Galaxy CloudMan instance by adding custom tools. I've
> installed my tools under the /mnt/galaxyTools/tools folder and I've modified
> the .bashrc files from the sgeadmin and galaxy users to add the needed paths
> to the PATH and PYTHONPATH variables. When I'm in Galaxy and I try to launch
> one of my tools, it fails and shows the 'Command not found' error.
> Where I should add the paths to make Galaxy now where are my executables?
> Whan I log into the isntance through ssh and I use the galaxy user, it knows
> where are my executables.
> What I'm missing?
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