Hey Kevin, 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. Best, Alper Kucukural, PhD Bioinformatics Core, University of Massachusetts Medical School 368 Plantation St.Room AS4.2067 Worcester, MA 01605-2324 Phone: 774-312-4493 E-mail: Alper.Kucukural@umassmed.edu On Aug 26, 2014, at 11:36 AM, Kevin <changk16@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 finish
dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation
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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