Hi All,

New to galaxy here. I'm having an issue uploading bam files into a local
instance of galaxy. I understand that it requires samtools, and I installed
the appropriate dependency from the toolshed. However, I get the following

Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
407, in <module>
  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
396, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line
324, 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
147, in dataset_content_needs_grooming
    version = self._get_samtools_version()
  File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
129, in _get_samtools_version
    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
stdout=subprocess.PIPE ).communicate()[1]
  File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

Which leads me to believe something is wrong with the install (can't
find samtools). The dependency directory is also set. Is there another
step I'm missing, or is it better to not install dependencies via the

Nathan Kipniss
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