Question: Problem uploading BAM file
0
stephane.roche • 10 wrote:
I have a problem after uploading a BAM file. This file have the state ERROR in my local installation of Galaxy whereas in a public distribution, it have not. I am working with an Xubuntu. Pyhthon 2.7.6 is installed. I suspect an problem with python interpreter.
Could you help me ?
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 407, in <module>
__main__()
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 145, in dataset_content_needs_grooming
version = self._get_samtools_version()
File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 127, 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
