Hi everybody,

This is not a big issue but I am curious to know about it:

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.

Cheers

Christophe

Christophe Antoniewski

Drosophila Genetics and Epigenetics
Laboratoire de Biolologie du Développement
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75252 Paris Cedex 05

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