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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