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
>

                                          
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