Question: Error: "Samtools not found" on a local Galaxy when running other jobs
0
gravatar for djevo1
14 months ago by
djevo160
djevo160 wrote:

I attempted to run a job using HISAT2 on galaxy and in the console it shows samtools not found, however the job finishes with a completed bam file. The issue is that galaxy marks the job with an error as unable to finish, even though it did successfully. Do I need to install samtools in the galaxy share for my cluster or is there another issue I may be having? Below is the last call.

Traceback (most recent call last):
  File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py", line 609, in finish_job
    job_state.job_wrapper.finish( stdout, stderr, exit_code )
  File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line 1274, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/datatypes/binary.py", line 355, in set_meta
    exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/usr/lib64/python2.7/subprocess.py", line 524, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson23k • written 14 months ago by djevo160
1
gravatar for y.hoogstrate
14 months ago by
y.hoogstrate450
Netherlands
y.hoogstrate450 wrote:

The hisat2 wrapper uses samtools for sorting the BAM file: https://github.com/galaxyproject/tools-iuc/blob/master/tools/hisat2/hisat2.xml#L86

However, it looks like this is - yet another - samtools dependency that galaxy needs to actually do the same (sorting, and indexing): http://mimodd.readthedocs.io/en/latest/install_galaxy.html#provide-your-galaxy-with-samtools-bcftools-executables

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L280 https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L324 https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L354

This requires that galaxy has access to samtools in its $PATH before starting up the Galaxy server.

I believe you need samtools 0.1.19 for this and not 1.* because the samtools sort commandline interface has changes and is not backwards compatible anymore.

At some point this should work out of the box and Galaxy should take care of this dependency automatically ( https://github.com/galaxyproject/galaxy/issues/2247 ) but for now just make sure it's available in $PATH

ADD COMMENTlink modified 14 months ago • written 14 months ago by y.hoogstrate450
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