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:re...@channing.harvard.edu
Date uploaded:2012-04-10
File size:626.5 Mb
Data type:auto
Build:?
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

error
Database/Build:?
Number of data lines:None
Disk file:/share/shared/galaxy-central-hbc/database/files/000/dataset_40.dat
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