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
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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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