I installed the bedtools tool from the public toolshed to my galaxy cluster. The jobs were failing because I hadn't installed the required binaries:

An error occurred running this job: /opt/sge/default/spool/execd/ip-10-194-50-118/job_scripts/2: line 13: genomeCoverageBed: command not found

Taking a closer look at the toolshed's page, I noticed there were a handful of required binaries (genomeCoverageBed, intersectBed, etc).

So I downloaded BEDTools and compiled all the binaries. I've put them in well organized directories using symlinks to specific versions, etc. The final executable directory containing symlinks to these binaries is "/mnt/galaxyTools/shed_tool_binaries/bin/".

I can make a snapshot of the tools volume so that these compiled binaries are always available to me when I bring up my cluster, but how do I integrate them into the PATH in a way that lets the bedtools galaxy tool see them, but also survive cluster shutdowns?

Thanks,

-Joel