It looks like the update didn't merge correctly and
shed_tool_data_table_conf.xml.sample (and potentially others, looking
at `hg diff run.sh` on a new instance, after updating to central's
tip) got left out of run.sh.

To fix this, you can update run.sh to include the files currently left out:

shed_tool_data_table_conf.xml.sample
data_manager_conf.xml.sample
shed_data_manager_conf.xml.sample

Or if you'd rather not tweak the startup script you can always just
copy those .sample files over to the root names (so, `cp
shed_tool_data_table_conf.xml.sample shed_tool_data_table_conf.xml`
for instance).

On Thu, Mar 21, 2013 at 4:05 PM, Brian Lin <brian....@tufts.edu> wrote:
> Hi, no problem at all, I'm still trying to get this to work, so the response
> was much appreciated!
> I setup a new vanilla instance, updated it, got the same error and then
> proceeded to restart it 3 more times.
> The galaxy log is pasted below. Any ideas on what might be going wrong?
> Thanks again!
> Brian
>
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,518 Loaded tool data table
> 'lastz_seqs'
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,518 Loaded tool data table
> 'perm_base_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,518 Loaded tool data table
> 'perm_color_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,518 Loaded tool data table
> 'sam_fa_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,519 Loaded tool data table
> 'picard_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,519 Loaded tool data table
> 'srma_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,519 Loaded tool data table
> 'tophat_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,519 Loaded tool data table
> 'mosaik_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,519 Loaded tool data table
> 'sam_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,520 Loaded tool data table
> 'twobit'
> galaxy.tools.data DEBUG 2013-03-21 18:00:55,520 Loaded tool data table
> 'lift_over'
> Traceback (most recent call last):
>   File
> "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py",
> line 37, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 93, in
> __init__
>     from_shed_config=True )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py",
> line 46, in load_from_config_file
>     tree = util.parse_xml( config_filename )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py", line
> 143, 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
> /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
> RuntimeWarning: __builtin__.file size changed, may indicate binary
> incompatibility
>   from csamtools import *
> python path is:
> /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.5.0-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Paste-1.7.5.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/,
> /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk,
> /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
> tool_shed.tool_shed_registry DEBUG 2013-03-21 18:03:20,620 Loading
> references to tool sheds from tool_sheds_conf.xml
> tool_shed.tool_shed_registry DEBUG 2013-03-21 18:03:20,620 Loaded reference
> to tool shed: Galaxy main tool shed
> tool_shed.tool_shed_registry DEBUG 2013-03-21 18:03:20,620 Loaded reference
> to tool shed: Galaxy test tool shed
> galaxy.model.migrate.check DEBUG 2013-03-21 18:03:20,640 psycopg2 egg
> successfully loaded for postgres dialect
> galaxy.model.migrate.check INFO 2013-03-21 18:03:20,782 At database version
> 114
> tool_shed.galaxy_install.migrate.check DEBUG 2013-03-21 18:03:20,793
> psycopg2 egg successfully loaded for postgres dialect
> tool_shed.galaxy_install.migrate.check INFO 2013-03-21 18:03:20,808 At
> migrate_tools version 7
> galaxy.model.custom_types DEBUG 2013-03-21 18:03:20,812 psycopg2 egg
> successfully loaded for postgres dialect
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,012 Loading datatypes
> from datatypes_conf.xml
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for
> datatype 'galaxy.datatypes.tabular:Vcf'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for
> datatype 'galaxy.datatypes.binary:TwoBit'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for
> datatype 'galaxy.datatypes.binary:Bam'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for
> datatype 'galaxy.datatypes.binary:Sff'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for
> datatype 'galaxy.datatypes.xml:Phyloxml'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for
> datatype 'galaxy.datatypes.xml:GenericXml'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Maf'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Lav'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:csFasta'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for
> datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for
> datatype 'galaxy.datatypes.qualityscore:QualityScore454'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Fasta'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Fastq'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Wiggle'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Html'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Pdf'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Axt'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Bed'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:CustomTrack'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Gtf'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Gff'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Gff3'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for
> datatype 'galaxy.datatypes.tabular:Pileup'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Interval'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for
> datatype 'galaxy.datatypes.tabular:Sam'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for
> datatype 'galaxy.datatypes.data:Newick'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for
> datatype 'galaxy.datatypes.data:Nexus'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Jpg'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Png'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Tiff'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Bmp'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Gif'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Im'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Pcd'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Pcx'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Ppm'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Psd'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Xbm'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Rgb'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Pbm'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Pgm'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Xpm'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,024 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Eps'
> galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,024 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Rast'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table
> 'all_fasta'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table
> 'blastdb'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table
> 'bowtie_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table
> 'bowtie_indexes_color'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table
> 'bwa_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table
> 'lastz_seqs'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table
> 'perm_base_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table
> 'perm_color_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table
> 'sam_fa_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table
> 'picard_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table
> 'srma_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table
> 'tophat_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table
> 'mosaik_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table
> 'sam_indexes'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,042 Loaded tool data table
> 'twobit'
> galaxy.tools.data DEBUG 2013-03-21 18:03:21,042 Loaded tool data table
> 'lift_over'
> Traceback (most recent call last):
>   File
> "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py",
> line 37, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 93, in
> __init__
>     from_shed_config=True )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py",
> line 46, in load_from_config_file
>     tree = util.parse_xml( config_filename )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py", line
> 143, 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
> /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
> RuntimeWarning: __builtin__.file size changed, may indicate binary
> incompatibility
>   from csamtools import *
> python path is:
> /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.5.0-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Paste-1.7.5.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/,
> /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk,
> /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
> tool_shed.tool_shed_registry DEBUG 2013-03-21 19:46:36,999 Loading
> references to tool sheds from tool_sheds_conf.xml
> tool_shed.tool_shed_registry DEBUG 2013-03-21 19:46:37,000 Loaded reference
> to tool shed: Galaxy main tool shed
> tool_shed.tool_shed_registry DEBUG 2013-03-21 19:46:37,000 Loaded reference
> to tool shed: Galaxy test tool shed
> galaxy.model.migrate.check DEBUG 2013-03-21 19:46:37,021 psycopg2 egg
> successfully loaded for postgres dialect
> galaxy.model.migrate.check INFO 2013-03-21 19:46:37,158 At database version
> 114
> tool_shed.galaxy_install.migrate.check DEBUG 2013-03-21 19:46:37,169
> psycopg2 egg successfully loaded for postgres dialect
> tool_shed.galaxy_install.migrate.check INFO 2013-03-21 19:46:37,185 At
> migrate_tools version 7
> galaxy.model.custom_types DEBUG 2013-03-21 19:46:37,188 psycopg2 egg
> successfully loaded for postgres dialect
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,399 Loading datatypes
> from datatypes_conf.xml
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,406 Loaded sniffer for
> datatype 'galaxy.datatypes.tabular:Vcf'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,406 Loaded sniffer for
> datatype 'galaxy.datatypes.binary:TwoBit'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,406 Loaded sniffer for
> datatype 'galaxy.datatypes.binary:Bam'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for
> datatype 'galaxy.datatypes.binary:Sff'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for
> datatype 'galaxy.datatypes.xml:Phyloxml'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for
> datatype 'galaxy.datatypes.xml:GenericXml'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Maf'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Lav'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:csFasta'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for
> datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for
> datatype 'galaxy.datatypes.qualityscore:QualityScore454'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Fasta'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Fastq'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Wiggle'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Html'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Pdf'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for
> datatype 'galaxy.datatypes.sequence:Axt'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Bed'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:CustomTrack'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Gtf'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Gff'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Gff3'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for
> datatype 'galaxy.datatypes.tabular:Pileup'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for
> datatype 'galaxy.datatypes.interval:Interval'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for
> datatype 'galaxy.datatypes.tabular:Sam'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for
> datatype 'galaxy.datatypes.data:Newick'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for
> datatype 'galaxy.datatypes.data:Nexus'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Jpg'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Png'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Tiff'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Bmp'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Gif'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Im'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Pcd'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Pcx'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Ppm'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Psd'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Xbm'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Rgb'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Pbm'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Pgm'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Xpm'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Eps'
> galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for
> datatype 'galaxy.datatypes.images:Rast'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,425 Loaded tool data table
> 'all_fasta'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table
> 'blastdb'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table
> 'bowtie_indexes'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table
> 'bowtie_indexes_color'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table
> 'bwa_indexes'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table
> 'lastz_seqs'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table
> 'perm_base_indexes'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table
> 'perm_color_indexes'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table
> 'sam_fa_indexes'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table
> 'picard_indexes'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table
> 'srma_indexes'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table
> 'tophat_indexes'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table
> 'mosaik_indexes'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table
> 'sam_indexes'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table
> 'twobit'
> galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table
> 'lift_over'
> Traceback (most recent call last):
>   File
> "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py",
> line 37, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 93, in
> __init__
>     from_shed_config=True )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py",
> line 46, in load_from_config_file
>     tree = util.parse_xml( config_filename )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py", line
> 143, 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
>
> --
> Brian Lin
> cont...@brian-lin.com
> brian....@tufts.edu
>
>
> On Thu, Mar 21, 2013 at 8:41 AM, Dannon Baker <dannon.ba...@gmail.com>
> wrote:
>>
>> Hey Brian,
>>
>> Sorry for the delayed response on this one, what you're seeing is a
>> consequence of how Galaxy's tool migration scripts work -- all you
>> should need to do is click restart one more time in the cloudman admin
>> UI.
>>
>> -Dannon
>>
>> On Thu, Mar 14, 2013 at 10:56 PM, Brian Lin <brian....@tufts.edu> wrote:
>> > Hi guys, I'm running into a problem with updating a completely squeaky
>> > clean
>> > fresh cloudman install using the current ami-da58aab3
>> > Once it is up and running, I have SSHed in and made sure the sample
>> > files in
>> > run.sh are complete.
>> > I hit the update button, and 3 or 4 minutes later when the daemon tries
>> > to
>> > restart, I get status= error.
>> > Is anyone else having this issue?? The only threads and posts I have
>> > found
>> > are from a year ago, and the line is in my run.sh.
>> > The ultimate goal of all this was just so that I could have a cufflinks
>> > version that is not 0.5.
>> >
>> > Thanks for any help anyone can provide.
>> >
>> > Brian
>> >
>> >
>> > Here are the logs:
>> >
>> > paster.log:
>> >
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
>> > RuntimeWarning: __builtin__.file size changed, may indicate binary
>> > incompatibility
>> >   from csamtools import *
>> > python path is:
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg,
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg,
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg,
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg,
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg,
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg,
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg,
>> >
>> > /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.5.0-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/eggs/Paste-1.7.5.1-py2.6.egg,
>> > /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/,
>> > /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk,
>> > /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
>> > tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loading
>> > references to tool sheds from tool_sheds_conf.xml
>> > tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded
>> > reference
>> > to tool shed: Galaxy main tool shed
>> > tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded
>> > reference
>> > to tool shed: Galaxy test tool shed
>> > galaxy.model.migrate.check DEBUG 2013-03-15 02:47:27,556 psycopg2 egg
>> > successfully loaded for postgres dialect
>> > galaxy.model.migrate.check INFO 2013-03-15 02:47:27,633 At database
>> > version
>> > 114
>> > tool_shed.galaxy_install.migrate.check DEBUG 2013-03-15 02:47:27,643
>> > psycopg2 egg successfully loaded for postgres dialect
>> > Traceback (most recent call last):
>> >   File
>> > "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py",
>> > line 37, in app_factory
>> >     app = UniverseApplication( global_conf = global_conf, **kwargs )
>> >   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 54, in
>> > __init__
>> >     verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
>> > '__file__', None ), self.config.database_engine_options )
>> >   File
>> >
>> > "/mnt/galaxyTools/galaxy-central/lib/tool_shed/galaxy_install/migrate/check.py",
>> > line 145, in verify_tools
>> >     raise Exception( msg )
>> > Exception:
>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>> >
>> > Console Log:
>> >
>> > 02:46:56 - Removing 'Galaxy' service
>> > 02:46:56 - Shutting down Galaxy...
>> > 02:47:25 - Starting Galaxy...
>> > 02:47:25 - Galaxy service state changed from 'Shut down' to 'Starting'
>> > 02:47:26 - Saved file 'persistent_data.yaml' to bucket
>> > 'cm-5b0fce1cf71e5f439fc17473dd4dcd1d'
>> > 02:48:28 - Galaxy daemon not running.
>> > 02:48:28 - Galaxy service state changed from 'Starting' to 'Error'
>> > 02:48:29 - Saved file 'persistent_data.yaml' to bucket
>> > 'cm-5b0fce1cf71e5f439fc17473dd4dcd1d'
>> > 02:49:30 - Galaxy daemon not running.
>> >
>> > pgSQL.log:
>> >
>> > LOG:  database system was shut down at 2013-03-15 02:11:48 UTC
>> > LOG:  autovacuum launcher started
>> > LOG:  database system is ready to accept connections
>> > ERROR:  relation "page_revision" does not exist
>> > STATEMENT:  ALTER TABLE page ADD CONSTRAINT page_latest_revision_id_fk
>> > FOREIGN KEY(latest_revision_id) REFERENCES page_revision (id)
>> > ERROR:  relation "visualization_revision" does not exist
>> > STATEMENT:  ALTER TABLE visualization ADD CONSTRAINT
>> > visualization_latest_revision_id_fk FOREIGN KEY(latest_revision_id)
>> > REFERENCES visualization_revision (id)
>> > LOG:  unexpected EOF on client connection
>> >
>> > SGE log:
>> >
>> > 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|read job database with 0
>> > entries in 0 seconds
>> > 03/15/2013 01:12:20|  main|ip-10-149-20-174|E|error opening file
>> > "/opt/sge/default/common/./sched_configuration" for reading: No such
>> > file or
>> > directory
>> > 03/15/2013 01:12:20|  main|ip-10-149-20-174|E|error opening file
>> > "/opt/sge/default/spool/qmaster/./sharetree" for reading: No such file
>> > or
>> > directory
>> > 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster hard descriptor
>> > limit
>> > is set to 8192
>> > 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster soft descriptor
>> > limit
>> > is set to 8192
>> > 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster will use max. 8172
>> > file descriptors for communication
>> > 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster will accept max.
>> > 99
>> > dynamic event clients
>> > 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|starting up GE 6.2u5
>> > (lx24-amd64)
>> > 03/15/2013 01:12:20|  main|ip-10-149-20-174|W|can't open job sequence
>> > number
>> > file "jobseqnum": for reading: No such file or directory -- guessing
>> > next
>> > number
>> > 03/15/2013 01:12:20|  main|ip-10-149-20-174|W|can't open ar sequence
>> > number
>> > file "arseqnum": for reading: No such file or directory -- guessing next
>> > number
>> > 03/15/2013 01:12:21|worker|ip-10-149-20-174|E|adminhost
>> > "ip-10-149-20-174.ec2.internal" already exists
>> > 03/15/2013 01:12:21|worker|ip-10-149-20-174|E|adminhost
>> > "ip-10-149-20-174.ec2.internal" already exists
>> > 03/15/2013 02:46:57|listen|ip-10-149-20-174|E|commlib error: got read
>> > error
>> > (closing "ip-10-149-20-174.ec2.internal/drmaa/416")
>> >
>> >
>> > --
>> > Brian Lin
>> > cont...@brian-lin.com
>> > brian....@tufts.edu
>> >
>> > ___________________________________________________________
>> > 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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