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 <BZeitner@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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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