It's likely that samtools is not in Galaxy's path because Trackster uses the same
path as Galaxy does. Also, many tools in Galaxy use the Galaxy PySam egg rather than the
samtools binary, so it's possible that you can run a tool that uses
"samtools" without the binary in Galaxy's path. Which tool were you able to
Probably the best idea is to simply convert SAM to BAM and then uses Trackster on the BAM.
Visualizing SAM datasets is occasionally problematic due to missing metadata and large
sizes, and SAM is simply converted to BAM before visualization anyways.
On Jul 2, 2012, at 9:37 AM, Yec'han Laizet wrote:
I try to use the visualization tool of my local instance of galaxy under
ubuntu. Everytime I try to create a feature track from a sam file, I get the
/bin/sh samtools not found
I have installed samtools from ubuntu reposotories and it works well as I can
call it from the shell. Nevertheless, I still get the same error.
I checked that the samtools binary is in a folder included in my $PATH as
I tried to use an "analyze data" tool in galaxy interface that uses samtools
and it worked.
It seems that it's only in trackster that samtools are not found.
Do you have an idea to fix it?
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