Question: Tophat: Samtools not found (but dependencies are installed)
gravatar for daniel.heredia
4.5 years ago by
United States
daniel.heredia0 wrote:

Could you give some tips for solve this error, please? All dependencies are installed, and samtools is in bin/sh indeed. We don't have idea what is going wrong. We had already try to reinstall packages and dependencies, change the path and more...


Traceback (most recent call last):
  File "/home/biostack/galaxy-dist/lib/galaxy/jobs/runners/", line 118, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/biostack/galaxy-dist/lib/galaxy/jobs/", line 963, 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/biostack/galaxy-dist/lib/galaxy/datatypes/", line 251, in set_meta
    raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found


Thanks and regards,

rna-seq tophat galaxy samtools bam • 2.7k views
ADD COMMENTlink modified 4.5 years ago by y.hoogstrate460 • written 4.5 years ago by daniel.heredia0

Is samtools executable? Is it also available in the $PATH where Galaxy is started? I do not think it has anything to do with the dependencies installed through the Tool Shed.

ADD REPLYlink written 4.5 years ago by Bjoern Gruening5.1k

yes, samtools is executable and $PATH is available.

ADD REPLYlink written 4.5 years ago by daniel.heredia0
gravatar for y.hoogstrate
4.5 years ago by
y.hoogstrate460 wrote:

Hi Daniel,

I'm not sure what's causing this and I have to admit that it seems that it's not reachable from $PATH. Does galaxy run under the same user as the one you have configured the $PATH for? Can you solve it by just adding a symlink to "/usr/local/bin/samtools" (if that one not already exists of course)?

What you can do to resolve the problem is to (temporary) modify the TopHat wrapper by adding to its command

echo $PATH > ~/tmp_dump_1.txt ; 

which samtools > ~/tmp_dump_2.txt ;

whoami > ~/tmp_dump_3.txt ;

... remainder of tophat command code


And check out if the files in your Desktop confirm what you expected

ADD COMMENTlink written 4.5 years ago by y.hoogstrate460
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