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 > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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