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  • Galaxy server fails to restart

    Hi ,

    Am trying to install local instance of Galaxy . After unzipping the source , server starts properly with ./run.sh --reload command . However after the process is killed and again server is restarted , it fails with following error .

    Traceback (most recent call last):
    File "/home/user1/NGS/galaxy-galaxy-central-f573461f3667/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
    File "/home/user1/NGS/galaxy-galaxy-central-f573461f3667/lib/galaxy/app.py", line 43, in __init__
    self._configure_models( check_migrate_databases=True, check_migrate_tools=True, config_file=config_file )
    File "/home/user1/NGS/galaxy-galaxy-central-f573461f3667/lib/galaxy/config.py", line 612, in _configure_models
    verify_tools( self, install_db_url, config_file, install_database_options )
    File "/home/user1/NGS/galaxy-galaxy-central-f573461f3667/lib/tool_shed/galaxy_install/migrate/check.py", line 61, in verify_tools
    latest_tool_migration_script_number )
    File "/home/user1/NGS/galaxy-galaxy-central-f573461f3667/lib/tool_shed/util/common_util.py", line 60, in check_for_missing_tools
    tool_shed_accessible, tool_dependencies = get_tool_dependencies( app, tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision )
    File "/home/user1/NGS/galaxy-galaxy-central-f573461f3667/lib/tool_shed/util/common_util.py", line 144, in get_tool_dependencies
    tool_dependencies_dict = encoding_util.tool_shed_decode( text )
    File "/home/user1/NGS/galaxy-galaxy-central-f573461f3667/lib/tool_shed/util/encoding_util.py", line 15, in tool_shed_decode
    a, b = value.split( ":" )
    ValueError: need more than 1 value to unpack


    Any idea if am missing out something . Also which version of Galaxy has samtools options integrated . The latest one have installed doesn't give me that .

    Thanks

  • #2
    See if this helps: http://user.list.galaxyproject.org/C...td4654767.html

    Also for galaxy admin related questions you should email (or search) Galaxy support list for quick help: http://dev.list.galaxyproject.org/

    Follow instructions here to install NGS related tools: https://wiki.galaxyproject.org/Admin...0Local%20Setup

    Comment


    • #3
      Originally posted by GenoMax View Post
      See if this helps: http://user.list.galaxyproject.org/C...td4654767.html

      Also for galaxy admin related questions you should email (or search) Galaxy support list for quick help: http://dev.list.galaxyproject.org/

      Follow instructions here to install NGS related tools: https://wiki.galaxyproject.org/Admin...0Local%20Setup
      Thanks .

      It didn't help me . Have posted the query to the dev.list and waiting for the reply .

      Thanks again .

      Comment

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