---

To: galaxy-dev@bx.psu.edu
From: liisa.koski@dnalandmarks.ca
Date: Tue, 20 Dec 2011 16:22:02 -0500
Subject: [galaxy-dev] Problem uploading files from filesystem paths

Hi,
I'm trying to upload data to Data Libraries from filesystems paths as Admin. I get the following error.
Any ideas?

Thanks in advance,
Liisa


Traceback (most recent call last): File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in __main__() File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in __main__ add_file( dataset, registry, js
Job Standard Error
Traceback (most recent call last):
 File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in
   __main__()
 File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in __main__
   add_file( dataset, registry, json_file, output_path )
 File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 300, in add_file
   if datatype.dataset_content_needs_grooming( dataset.path ):
 File "/data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming
   version = self._get_samtools_version()
 File "/data/Galaxy/galaxy-dist/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/lib64/python2.6/subprocess.py", line 633, in __init__
   errread, errwrite)
 File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child
   raise child_exception
OSError: [Errno 13] Permission denied


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