Hello,
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 run successfully?
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.
Best,
J.
On Jul 2, 2012, at 9:37 AM, Yec'han Laizet wrote:
Hello,
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
following error:
/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
described here:
http://dev.list.galaxyproject.org/Re-bin-sh-samtools-not-found-gt-gt-
WORKAROUND-td4585265.html
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?
Best regards
Yec'han
Yec'han LAIZET
Ingénieur
Plateforme Genome Transcriptome
Tel: 05 57 12 27 75
_
INRA-UMR BIOGECO 1202
Equipe Genetique
69 route d'Arcachon
33612 CESTAS
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