Hi Dev Team,
I am attempting to get a new/clean installation running and am having difficulty. I did a clone from https://bitbucket.org/galaxy/galaxy-dist and made my needed configuration changes for my environment. I attempted to start it and needed to do the database upgrade via sh manage_db.sh upgrade. That went just fine. I tried another start and got the following error:
migrate.versioning.repository DEBUG 2014-07-17 13:07:56,566 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_tools', 'repository_id': 'GalaxyTools'}} tool_shed.galaxy_install.migrate.check DEBUG 2014-07-17 13:07:56,571 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line 46, in __init__ self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/config.py", line 656, in _configure_models verify_tools( self, install_db_url, config_file, install_database_options ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/migrate/check.py", line 150, in verify_tools raise Exception( msg ) Exception:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The list of files at the end of this message refers to tools that are configured to load into the tool panel for this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this, be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should be removed from your file named ./tool_conf.xml.
CRITICAL NOTE IF YOU PLAN TO INSTALL The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool> tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following URL for details.
http://mercurial.selenic.com/wiki/.hgignore
The following tool dependencies can also optionally be installed (see the option flag in the command below). If you choose to install them (recommended), they will be installed within the location specified by the 'tool_dependency_dir' setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini). ------------------------------------ Tool Dependency ------------------------------------ Name: bx-python, Version: 0.7.1, Type: package
------------------------------------ ------------------------------------ Tool Dependency ------------------------------------ Name: R, Version: 2.11.0, Type: package
------------------------------------ ------------------------------------ Tool Dependency ------------------------------------ Name: rpy, Version: 1.0.3, Type: package
------------------------------------ ------------------------------------ Tool Dependency ------------------------------------ Name: numpy, Version: 1.7.1, Type: package
------------------------------------ ------------------------------------ Tool Dependency ------------------------------------ Name: yacca, Version: 1.0, Type: package
------------------------------------ ------------------------------------ Tool Dependency ------------------------------------ Name: kernlab, Version: 0.1-4, Type: package
------------------------------------ ------------------------------------ Tool Dependency ------------------------------------ Name: libxml2, Version: 2.9.1, Type: package
------------------------------------ ------------------------------------ Tool Dependency ------------------------------------ Name: libpng, Version: 1.6.7, Type: package
------------------------------------ ------------------------------------ Tool Dependency ------------------------------------ Name: fontconfig, Version: 2.11.1, Type: package
------------------------------------ ------------------------------------ Tool Dependency ------------------------------------ Name: blast+, Version: 2.2.26+, Type: package
------------------------------------
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://<user>:<pass>@<host>/<dbname> vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0011_tools.sh ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies' option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv sh ./scripts/migrate_tools/0011_tools.sh install_dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process, entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been removed from your file named ./tool_conf.xml.
fasta_to_tabular.xml tabular_to_fasta.xml annotation_profiler.xml pca.xml cca.xml kpca.xml kcca.xml fasta_compute_length.xml fasta_filter_by_length.xml fasta_concatenate_by_species.xml short_reads_figure_score.xml short_reads_trim_seq.xml megablast_wrapper.xml megablast_xml_parser.xml <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Removing PID file manager.pid
I ignored that since it is related to a config file I copied from my previous instance. I retried another start and I get the following:
migrate.versioning.repository DEBUG 2014-07-17 13:09:59,145 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_tools', 'repository_id': 'GalaxyTools'}} tool_shed.galaxy_install.migrate.check DEBUG 2014-07-17 13:09:59,161 psycopg2 egg successfully loaded for postgres dialect tool_shed.galaxy_install.migrate.check INFO 2014-07-17 13:09:59,215 At migrate_tools version 11 galaxy.model.orm DEBUG 2014-07-17 13:09:59,224 psycopg2 egg successfully loaded for postgres dialect galaxy.config INFO 2014-07-17 13:09:59,251 Install database targetting Galaxy's database configuration. sqlalchemy.pool.QueuePool WARNING 2014-07-17 13:10:01,869 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block
Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line 52, in __init__ self._configure_datatypes_registry( self.installed_repository_manager ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/config.py", line 605, in _configure_datatypes_registry installed_repository_manager.load_proprietary_datatypes() File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", line 278, in load_proprietary_datatypes .order_by( self.install_model.ToolShedRepository.table.c.id ): File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py", line 2227, in __iter__ return self._execute_and_instances(context) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py", line 2242, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement compiled_sql, distilled_params File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1698, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1691, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 331, in do_execute cursor.execute(statement, parameters) ProgrammingError: (ProgrammingError) column tool_shed_repository.status does not exist LINE 1: ...ist_to_shed AS tool_shed_repository_dist_to_shed, tool_shed_... ^ 'SELECT tool_shed_repository.id AS tool_shed_repository_id, tool_shed_repository.create_time AS tool_shed_repository_create_time, tool_shed_repository.update_time AS tool_shed_repository_update_time, tool_shed_repository.tool_shed AS tool_shed_repository_tool_shed, tool_shed_repository.name AS tool_shed_repository_name, tool_shed_repository.description AS tool_shed_repository_description, tool_shed_repository.owner AS tool_shed_repository_owner, tool_shed_repository.installed_changeset_revision AS tool_shed_repository_installed_changeset_revision, tool_shed_repository.changeset_revision AS tool_shed_repository_changeset_revision, tool_shed_repository.ctx_rev AS tool_shed_repository_ctx_rev, tool_shed_repository.metadata AS tool_shed_repository_metadata, tool_shed_repository.includes_datatypes AS tool_shed_repository_includes_datatypes, tool_shed_repository.tool_shed_status AS tool_shed_repository_tool_shed_status, tool_shed_repository.deleted AS tool_shed_repository_deleted, tool_shed_repository.uninstalled AS tool_shed_repository_uninstalled, tool_shed_repository.dist_to_shed AS tool_shed_repository_dist_to_shed, tool_shed_repository.status AS tool_shed_repository_status, tool_shed_repository.error_message AS tool_shed_repository_error_message \nFROM tool_shed_repository \nWHERE tool_shed_repository.includes_datatypes = %(includes_datatypes_1)s AND tool_shed_repository.deleted = %(deleted_1)s ORDER BY tool_shed_repository.id' {'includes_datatypes_1': True, 'deleted_1': False} Removing PID file manager.pid
Can someone point me to a resolution?
Thanks, __________________________________ Iry T. Witham Scientific Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham@jax.org
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