Hello,

I’m running a local installation of galaxy. While loading a bam file (2GB) to galaxy, I get the following error:

Traceback (most recent call last):

  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 403, in <module>

    __main__()

  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 392, in __main__

    add_file( dataset, registry, json_file, output_path )

  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 331, in add_file

    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):

  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming

    version = self._get_samtools_version()

  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, 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 1220, in _execute_child

    raise child_exception

OSError: [Errno 2] No such file or directory

I’ve succeeded to execute other commands that used samtools.

I’ve also succeeded in running the command:

subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]

in python on the server which galaxy installed on, logged in to the user under which galaxy is executed.

Do you have any idea what can cause it, and how to solve the problem?

Maya