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: [email protected]
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