Question: unable to upload bam files to my local galaxy instance - SAMtools not found
0
gravatar for kvoutet
4.2 years ago by
kvoutet0
National Hellenic Research Foundation
kvoutet0 wrote:

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:///)
rna-seq software error • 1.3k views
ADD COMMENTlink modified 4.1 years ago • written 4.2 years ago by kvoutet0

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

ADD REPLYlink written 4.2 years ago by Tonor430
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.
ADD REPLYlink modified 4.2 years ago by Devon Ryan98k • written 4.2 years ago by kvoutet0

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

ADD REPLYlink written 4.2 years ago by Devon Ryan98k

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

ADD REPLYlink written 4.1 years ago by kvoutet0

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

ADD REPLYlink written 4.1 years ago by kvoutet0
1

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)?

ADD REPLYlink written 4.1 years ago by GenoMax95k
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