I believe Galaxy requires samtools to be installed to work with bam data. If you install samtools in a location Galaxy can see it then this error should no longer occur. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Jan 25, 2013 at 11:11 AM, Maureen J. Donlin <donlinmj@slu.edu> wrote:
Hi,
I tried to load a BAM file into our local instance of Galaxy but get the following error. I had preloaded the genome to which it was aligned and the bai file. Do I have to load these using a different method and the file upload?
Thanks, Maureen
Traceback error:
Traceback (most recent call last): File "/work/apps/galaxy/tools/data_source/upload.py", line 384, in <module> __main__() File "/work/apps/galaxy/tools/data_source/upload.py", line 373, in __main__ add_file( dataset, registry, json_file, output_path ) File "/work/apps/galaxy/tools/data_source/upload.py", line 312, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/work/apps/galaxy/lib/galaxy/datatypes/binary.py", line 113, in dataset_content_needs_grooming version = self._get_samtools_version() File "/work/apps/galaxy/lib/galaxy/datatypes/binary.py", line 97, 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 1228, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
-- Maureen J. Donlin, Ph.D. Research Associate Professor Dept. of Biochemistry & Molecular Biology Dept. of Molecular Microbiology & Immunology Saint Louis University School of Medicine 507 Doisy Research Center Office: 314-977-8858 Cell: 314-750-2345
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