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:[email protected] 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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