> 
> To have Trackster visualization working properly in Galaxy, one needs 
> bedtools.
> Yet in our instance (running under Ubuntu OS), installing bedtools in the 
> galaxy home directory and setting the environmental variable PATH in the 
> .profile file so that it includes the path to ~/bin/bedtools does not work.
> Yet the PATH variable is indeed including the appropriate information as the 
> owner of the galaxy home directory can run the bedtools in command lines.
> I have also to precise that we use a lot of third party tools (bowtie, 
> cufflinks, etc...) including wigToBigWig which is also required for 
> trackster, and that we have no path problem with these tools.
> 
> Indeed the only way to get galaxy accessing properly to the bedtools 
> currently is to put the bedtools in the /usr/local/bin directory. Here it 
> works !
> 
> I suspect it is a problem of shell specification when the bedtools are used 
> for trackster, but I could not figure out further the issue.

It's difficult to speculate about what's going on. 

Trackster uses the same infrastructure (PATH, submission script, etc.) for 
running bedtools that other Galaxy tools use, so there's reason to think that 
Trackster requires something special in any way. I also have multiple instances 
where bedtools is installed alongside bowtie/cufflinks/tophat/wigToBigWig/etc. 
in a single bin directory that is in the Galaxy user's path, and that works for 
me.

You could certainly modify the conversion tools that Trackster uses to echo and 
inspect the PATH. Let us know if you find anything interesting.

Best,
J.
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