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
> >
> > 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.
>
--
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
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
