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.kucuku...@umassmed.edu
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 > 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 > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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