Hi,

I tried to load a BAM file into our local instance of Galaxy but get the following error. I had preloaded the genome to which it was aligned and the bai file. Do I have to load these using a different method and the file upload?

Thanks,
Maureen

Traceback error:

Traceback (most recent call last):
  File "/work/apps/galaxy/tools/data_source/upload.py", line 384, in <module>
    __main__()
  File "/work/apps/galaxy/tools/data_source/upload.py", line 373, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/work/apps/galaxy/tools/data_source/upload.py", line 312, in add_file
    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
  File "/work/apps/galaxy/lib/galaxy/datatypes/binary.py", line 113, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/work/apps/galaxy/lib/galaxy/datatypes/binary.py", line 97, in _get_samtools_version
    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
  File "/usr/lib64/python2.6/subprocess.py", line 639, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.6/subprocess.py", line 1228, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

--
Maureen J. Donlin, Ph.D.
Research Associate Professor
Dept. of Biochemistry & Molecular Biology
Dept. of Molecular Microbiology & Immunology
Saint Louis University School of Medicine
507 Doisy Research Center
Office: 314-977-8858
Cell: 314-750-2345