Hi Brad,
In your Galaxy installation directory, try copying
shed_tool_data_table_conf.xml.sample to shed_tool_data_table_conf.xml.
Hopefully that will resolve the problem.
Greg Von Kuster
On Jun 26, 2013, at 6:22 PM, Brad Zeitner bzeit...@benaroyaresearch.org wrote:
I've started up an instance using cloudman, and it seemed to be running fine.
When I tried to install a tool from the toolshed I got an error, and in
trying to resolve the error I used the admin console to update galaxy.
Now when Galaxy tries to start I get the following error:
galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for
datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for
datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for
datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for
datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for
datatype 'galaxy.datatypes.images:Rast'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table
'all_fasta'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table
'blastdb'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table
'bowtie_indexes'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table
'bowtie_indexes_color'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table
'bwa_indexes'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table
'lastz_seqs'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table
'perm_base_indexes'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table
'perm_color_indexes'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table
'sam_fa_indexes'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table
'picard_indexes'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table
'srma_indexes'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table
'tophat_indexes'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table
'mosaik_indexes'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table
'sam_indexes'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table
'twobit'
galaxy.tools.data DEBUG 2013-06-26 22:20:49,999 Loaded tool data table
'lift_over'
Traceback (most recent call last):
File
/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py, line
35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /mnt/galaxyTools/galaxy-central/lib/galaxy/app.py, line 95, in
__init__
from_shed_config=False )
File /mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py,
line 56, in load_from_config_file
tree = util.parse_xml( config_filename )
File /mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py, line
132, in parse_xml
tree = ElementTree.parse(fname)
File
/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py,
line 859, in parse
tree.parse(source, parser)
File
/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py,
line 576, in parse
source = open(source, rb)
IOError: [Errno 2] No such file or directory:
'./shed_tool_data_table_conf.xml'
Removing PID file paster.pid
How do I resolve the no such file or directory error?
I found an email conversation on this that said to restart galaxy, and I've
done this multiple times but the problem is persisting.
Thanks,
-Brad
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