Path to the bedtools for getting trackster working properly
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 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org
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.
My fault my own fault ! Our galaxy instance is running as a service. I forgot to modify the export path command in the galaxy daemon config file which we setup in the /etc/init.d directory Shame on me Chris 2013/6/26 Jeremy Goecks <jeremy.goecks@emory.edu>
To have Trackster visualization working properly in Galaxy, one needs
Yet in our instance (running under Ubuntu OS), installing bedtools in
Yet the PATH variable is indeed including the appropriate information as
I have also to precise that we use a lot of third party tools (bowtie, cufflinks, etc...) including wigToBigWig which is also required for
bedtools. 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. the owner of the galaxy home directory can run the bedtools in command lines. 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.
-- Christophe Antoniewski Drosophila Genetics and Epigenetics Laboratoire de Biolologie du Développement 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 http://drosophile.org
participants (2)
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Christophe Antoniewski -
Jeremy Goecks