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Old 07-22-2014, 10:59 AM   #1
leontp587
Junior Member
 
Location: US

Join Date: Jul 2014
Posts: 6
Default Galaxy import BAM file error

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
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Old 07-22-2014, 11:16 AM   #2
wolma
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Location: Germany

Join Date: May 2014
Posts: 23
Default

When you import a bam file, Galaxy is trying to call samtools to check the file's content (to "groom" it as it's called in Galaxy)

This part of the error message:

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

means that samtools wasn't found, which could be either because you haven't installed it or because it's in a directory that's not in your system PATH.

Think of Galaxy as a framework. It provides user-friendly access to command line tools (like samtools), but you still have to install these tools.

Best,
Wolfgang
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Old 07-22-2014, 11:28 AM   #3
wolma
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Location: Germany

Join Date: May 2014
Posts: 23
Default

By the way,
there is an excellent Galaxy-specific forum at https://biostar.usegalaxy.org/ .
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