hello,

I am installing  galaxy locally.

I tried to upload a  ".bam" file and I got this message:

Traceback (most recent call last):
  File "/home/user/galaxy_project/tools/data_source/upload.py", line 386, in <module>
    __main__()
  File "/home/user/galaxy_project/tools/data_source/upload.py", line 375, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/home/user/galaxy_project/tools/data_source/upload.py", line 314, in add_file
    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
  File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 113, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/home/user/galaxy_project/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/lib/python2.7/subprocess.py", line 679, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1259, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

This file uploaded  successfully, to the galaxy on the net.

what can it be?

 thanks for your help

merav

 

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