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
To try and fix the problem, I moved the samtools executable into the TopHat2 /bin, I also went into the “universe_wsgi.ini” and uncommented+changed the line “retry_metadata_internally=true” to “retry_metadata_internally=false”.
Then, when I ran the TopHat2 alignment again, the job was able to be completed. However, now the only problem is a small notification under the "Accepted Hits" file saying that “An error occurred setting the metadata for this dataset. You may be able to set it manually or retry auto-detection”. When I tried to run Cufflinks using this file, it showed an error about not correctly setting the metadata for file.
Does anyone have any suggestions about how I could possibly fix this problem? I have practically done everything I could think of to solve this problem, but I have run into a wall.
Thanks and any advice is highly appreciated!