I installed my own copy of Galaxy on my local computer. It runs very well, I modified the universe_wsgi.ini file to allow for uploading of bam files from the system path.
So, when I tried to add a bam file to the shared library as admin, I get the error below. Anybody know what is going on here? It's a 55GB bam file.
Traceback (most recent call last):
File "/home/leon/galaxy-dist/tools/data_source/upload.py", line 394, in
__main__()
File "/home/leon/galaxy-dist/tools/data_source/upload.py", line 383, in __main__
add_file( dataset, registry, json_file, output_path )
File "/home/leon/galaxy-dist/tools/data_source/upload.py", line 292, in add_file
if datatype.dataset_content_needs_grooming( dataset.path ):
File "/home/leon/galaxy-dist/lib/galaxy/datatypes/binary.py", line 148, in dataset_content_needs_grooming
version = self._get_samtools_version()
File "/home/leon/galaxy-dist/lib/galaxy/datatypes/binary.py", line 130, in _get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
error
Database/Build: ?
BAM Index File: None
Disk file: /home/leon/genome_data/hu80855C/PG0001217-BLD.bam
So, when I tried to add a bam file to the shared library as admin, I get the error below. Anybody know what is going on here? It's a 55GB bam file.
Traceback (most recent call last):
File "/home/leon/galaxy-dist/tools/data_source/upload.py", line 394, in
__main__()
File "/home/leon/galaxy-dist/tools/data_source/upload.py", line 383, in __main__
add_file( dataset, registry, json_file, output_path )
File "/home/leon/galaxy-dist/tools/data_source/upload.py", line 292, in add_file
if datatype.dataset_content_needs_grooming( dataset.path ):
File "/home/leon/galaxy-dist/lib/galaxy/datatypes/binary.py", line 148, in dataset_content_needs_grooming
version = self._get_samtools_version()
File "/home/leon/galaxy-dist/lib/galaxy/datatypes/binary.py", line 130, in _get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
error
Database/Build: ?
BAM Index File: None
Disk file: /home/leon/genome_data/hu80855C/PG0001217-BLD.bam
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