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 <donli...@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: > > http://lists.bx.psu.edu/ ___________________________________________________________ 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: http://lists.bx.psu.edu/
