unable to upload bam files to my local galaxy instance - SAMtools not found

Question

[kvoutet]

I have download via Toolshed samtools 0.1.19 and 1.2 to my local galaxy and I have set the PATH to my $PATH but unfortunately I take the following error all the time. Please help!

galaxy.jobs DEBUG 2016-11-29 11:28:19,961 (11) Working directory for job is: /home/user/galaxy/database/jobs_directory/000/11
galaxy.jobs.handler DEBUG 2016-11-29 11:28:20,005 (11) Dispatching to local runner
galaxy.jobs DEBUG 2016-11-29 11:28:20,133 (11) Persisting job destination (destination id: local:///)
galaxy.jobs.runners DEBUG 2016-11-29 11:28:20,171 Job [11] queued (165.558 ms)
galaxy.jobs.handler INFO 2016-11-29 11:28:20,238 (11) Job dispatched
galaxy.tools.deps DEBUG 2016-11-29 11:28:20,817 Building dependency shell command for dependency 'samtools'
galaxy.tools.deps DEBUG 2016-11-29 11:28:20,818 Find dependency samtools version None
galaxy.tools.deps DEBUG 2016-11-29 11:28:20,818 Dependency samtools not found.
galaxy.tools.deps WARNING 2016-11-29 11:28:20,818 Failed to resolve dependency on 'samtools', ignoring
galaxy.jobs.command_factory INFO 2016-11-29 11:28:20,899 Built script [/home/user/galaxy/database/jobs_directory/000/11/tool_script.sh] for tool command[python /home/user/galaxy/tools/data_source/upload.py /home/user/galaxy /home/user/galaxy/database/tmp/tmpClvw1R /home/user/galaxy/database/tmp/tmpQBfoHp 33:/home/user/galaxy/database/jobs_directory/000/11/dataset_33_files:None]
galaxy.tools.deps DEBUG 2016-11-29 11:28:21,314 Building dependency shell command for dependency 'samtools'
galaxy.tools.deps DEBUG 2016-11-29 11:28:21,315 Find dependency samtools version None
galaxy.tools.deps DEBUG 2016-11-29 11:28:21,315 Dependency samtools not found.
galaxy.tools.deps WARNING 2016-11-29 11:28:21,315 Failed to resolve dependency on 'samtools', ignoring
galaxy.jobs.runners DEBUG 2016-11-29 11:28:21,355 (11) command is: mkdir -p working; cd working; /home/user/galaxy/database/jobs_directory/000/11/tool_script.sh; return_code=$?; cd '/home/user/galaxy/database/jobs_directory/000/11'; python "/home/user/galaxy/database/jobs_directory/000/11/set_metadata_USDwaV.py" "/home/user/galaxy/database/tmp/tmpClvw1R" "/home/user/galaxy/database/jobs_directory/000/11/working/galaxy.json" "/home/user/galaxy/database/jobs_directory/000/11/metadata_in_LibraryDatasetDatasetAssociation_33_exz1Ca,/home/user/galaxy/database/jobs_directory/000/11/metadata_kwds_LibraryDatasetDatasetAssociation_33_iI1DvX,/home/user/galaxy/database/jobs_directory/000/11/metadata_out_LibraryDatasetDatasetAssociation_33_gZSiib,/home/user/galaxy/database/jobs_directory/000/11/metadata_results_LibraryDatasetDatasetAssociation_33_1tS0Ua,/home/user/media/NGS/miRNAseq_U87_cells/Known_miRNAs/results/results_new/Bowtie1_results/Sample_9_R1_clean_nat_bw1.bam,/home/user/galaxy/database/jobs_directory/000/11/metadata_override_LibraryDatasetDatasetAssociation_33_4JvzzE" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2016-11-29 11:28:21,400 (11) executing job script: /home/user/galaxy/database/jobs_directory/000/11/galaxy_11.sh
galaxy.jobs DEBUG 2016-11-29 11:28:21,438 (11) Persisting job destination (destination id: local:///)

[Tonor]

Prob worth trying the galaxy biostars: https://biostar.usegalaxy.org

[kvoutet]

Traceback (most recent call last):
  File "/home/user/galaxy/tools/data_source/upload.py", line 434, in <module>
    __main__()
  File "/home/user/galaxy/tools/data_source/upload.py", line 423, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/home/user/galaxy/tools/data_source/upload.py", line 317, in add_file
    if datatype.dataset_content_needs_grooming( dataset.path ):
  File "/home/user/galaxy/lib/galaxy/datatypes/binary.py", line 251, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/home/user/galaxy/lib/galaxy/datatypes/binary.py", line 212, in _get_samtools_version
    raise Exception(message)
Exception: Attempting to use functionality requiring samtools, but it cannot be located on Galaxy's PATH.

[Devon Ryan]

Did you restart Galaxy after adjusting the $PATH? Making the adjustment in a different shell won't suffice.

[kvoutet]

Yes, I restarted Galaxy after adjustment in the same shell.

[kvoutet]

Please help!!!I have consumed a lot of time to resolve this issue but nothing...the same error!

[GenoMax]

Have you tried posting to Galaxy biostars as was suggested before? Are you able to locate samtools in the shell you are starting galaxy from (which samtools)?