Hello,

I set the library_import_dir setting in my universe_wsgi.ini file so that I could upload a directory of files into galaxy. I'm getting the following error screen when I attempt the upload from /tmp. The permissions are that galaxy owns the files in /tmp. I get the same error message when I try to upload the files from my computer.

-rw-r--r-- 1 galaxy stapusr 656960285 Apr 10 14:36 117681r.bam

Uploaded by:rerpc@channing.harvard.edu

Date uploaded:2012-04-10

Miscellaneous information:uploaded bam fileTraceback (most recent call last): File "/share/shared/galaxy-central-hbc/tools/data_source/upload.py", line 410, in __main__() File "/share/shared/galaxy-central-hbc/tools/data_source/upload.py", line 399, in __main__

Job Standard Error

Traceback (most recent call last):
  File "/share/shared/galaxy-central-hbc/tools/data_source/upload.py", line 410, in 

    __main__()
  File "/share/shared/galaxy-central-hbc/tools/data_source/upload.py", line 399, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/share/shared/galaxy-central-hbc/tools/data_source/upload.py", line 338, in add_file

    if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
  File "/share/shared/galaxy-central-hbc/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming

    version = self._get_samtools_version()
  File "/share/shared/galaxy-central-hbc/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version
    output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]

  File "/usr/local/python27/lib/python2.7/subprocess.py", line 672, in __init__
    errread, errwrite)
  File "/usr/local/python27/lib/python2.7/subprocess.py", line 1202, in _execute_child
    raise child_exception


OSError: [Errno 13] Permission denied