Sorry for bumping this, but it seems like such a standard boilerplate step of installing a tool that someone muts know how. -Joel
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