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 

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?


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