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
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: