Thanks for the response.
Samtools was installed, but there was an issue with it running on our cluster versus locally. Our sysadmin has temporarily disabled the calls to the cluster until he can work out those issues. It works fine now that it's running locally.


Regards,
Maureen

On 1/30/13 12:24 PM, James Taylor wrote:
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

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--
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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