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
contact@brian-lin.com
brian.lin@tufts.edu


On Thu, Mar 21, 2013 at 8:41 AM, Dannon Baker <dannon.baker@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.Lin@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
> contact@brian-lin.com
> brian.lin@tufts.edu
>
> ___________________________________________________________
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