I'm having issues uploading bam files to our galaxy server. It fails for both FTP and browser upload. Upload.py is executed on the local job runner.

The error is:

Traceback (most recent call last):
  File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 390, in <module>
  File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 379, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/galaxy/galaxy-dist/tools/data_source/upload.py", line 318, in add_file
    if link_data_only == 'copy_files' and 
datatype.dataset_content_needs_grooming( output_path ):
  File "/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 144, in 
    version = self._get_samtools_version()
  File "/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 128, in 
    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, 
stdout=subprocess.PIPE ).communicate()[1]
  File "/usr/lib/python2.6/subprocess.py", line 633, in __init__
    errread, errwrite)
  File "/usr/lib/python2.6/subprocess.py", line 1139, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

The logs show 'galaxy.tools.deps WARNING 2014-05-05 15:39:20,676 Failed to 
resolve dependency on 'samtools', ignoring'

I do have samtools in my path (~/bin/samtools).

Also, the file is actually uploaded fine (can be downloaded again correctly), 
but cannot be used in galaxy due to its 'error' state.

Any advice on how to solve this?




Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be

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