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