You need to install samtools and bowtie(2) into your system. I assume, the
package you installed to galaxy is just a wrapper to call samtools. It doesn’t
come with samtools binary.
Alper Kucukural, PhD
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
On Aug 26, 2014, at 11:36 AM, Kevin <chang...@byramhills.net> wrote:
> Hello All,
> I am running a Galaxy instance on Linux and have installed tools from the
> Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable
> to complete the job before I get the following error message:
> Traceback (most recent call last):
> File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129,
> in queue_job
> job_wrapper.finish( stdout, stderr, exit_code )
> File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in
> dataset.datatype.set_meta( dataset, overwrite=False ) # call
> datatype.set_meta directly for the initial set_meta call during dataset
> File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251,
> in set_meta
> raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
> So far, I have made sure that the samtools do appear to be installed since
> they can be found listed under "Managed Installed Tool Shed Repositories". Is
> it possible that they were installed incorrectly?
> Any help is much appreciated.
> Thanks for taking the time to read this,
> Kevin Chang
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