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 runtime. -Dannon 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? > > Thanks, > Jose > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
