Seems like an error concerning permissions in your galaxy folders. Try:
sudo chmod 777 galaxy-dist/
and then try to upload data again.
To: galaxy-...@bx.psu.edu
From: liisa.ko...@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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