[root - galaxy-dist]# ./run_functional_tests.sh
/home/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/other_packages/_mechanize_dist/_auth.py:14: DeprecationWarning: the md5 module is deprecated; use hashlib instead
  import re, base64, urlparse, posixpath, md5, sha, sys, copy
/home/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/other_packages/_mechanize_dist/_auth.py:14: DeprecationWarning: the sha module is deprecated; use the hashlib module instead
  import re, base64, urlparse, posixpath, md5, sha, sys, copy
/home/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/other_packages/_mechanize_dist/_msiecookiejar.py:255: SyntaxWarning: assertion is always true, perhaps remove parentheses?
  assert (sig in ("HASH", "LEAK",
/home/galaxy/galaxy-dist/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 *
[('app:main', 'datatype_converters_config_file', 'datatype_converters_conf.xml.sample'), ('app:main', 'new_file_path', '/tmp/tmpAntFXD/tmpxBWOfe/new_files_path_ElYcSt'), ('app:main', 'database_connection', 'sqlite:////tmp/tmpAntFXD/tmpxBWOfe/database/universe.sqlite'), ('app:main', 'job_queue_workers', 5), ('app:main', 'log_destination', 'stdout'), ('app:main', 'id_secret', 'changethisinproductiontoo'), ('app:main', 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml'), ('app:main', 'allow_user_deletion', True), ('app:main', 'update_integrated_tool_panel', False), ('app:main', 'tool_config_file', 'tool_conf.xml'), ('app:main', 'admin_users', 'test@bx.psu.edu'), ('app:main', 'job_working_directory', '/tmp/tmpAntFXD/tmpxBWOfe/job_working_directory_OZTdWT'), ('app:main', 'template_path', 'templates'), ('app:main', 'allow_user_creation', True), ('app:main', 'use_heartbeat', False), ('app:main', 'allow_library_path_paste', True), ('app:main', 'running_functional_tests', True), ('app:main', 'test_conf', 'test.conf'), ('app:main', 'tool_path', 'tools'), ('app:main', 'tool_data_table_config_path', 'tool_data_table_conf.xml'), ('app:main', 'tool_parse_help', False), ('app:main', 'user_library_import_dir', '/home/galaxy/galaxy-dist/test-data/users'), ('app:main', 'library_import_dir', '/home/galaxy/galaxy-dist/test-data'), ('app:main', 'file_path', '/tmp/tmpAntFXD/tmpxBWOfe/database/files')]
python path is: /home/galaxy/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, /home/galaxy/galaxy-dist/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /home/galaxy/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /home/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /home/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /home/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/other_packages, /home/galaxy/galaxy-dist/eggs/pysqlite-2.5.6_3.6.17_static-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/PasteDeploy-1.5.0-py2.6.egg, /home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg, /home/galaxy/galaxy-dist/eggs/NoseTestDiff-0.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/NoseHTML-0.4.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/nose-0.11.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /home/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /home/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /home/galaxy/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /home/galaxy/galaxy-dist/lib, /home/galaxy/galaxy-dist/lib, /home/galaxy/galaxy-dist/test, /usr/lib64/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info, /home/galaxy/galaxy-dist, /usr/lib/python2.6/site-packages, /home/galaxy/galaxy-dist/eggs/twill-0.9-py2.6.egg/twill/extensions, /usr/lib64/python2.6/site-packages
tool_shed.tool_shed_registry DEBUG 2013-12-19 12:18:18,062 Loading references to tool sheds from tool_sheds_conf.xml
tool_shed.tool_shed_registry DEBUG 2013-12-19 12:18:18,062 Loaded reference to tool shed: Galaxy main tool shed
tool_shed.tool_shed_registry DEBUG 2013-12-19 12:18:18,062 Loaded reference to tool shed: Galaxy test tool shed
migrate.versioning.repository DEBUG 2013-12-19 12:18:18,168 Loading repository lib/galaxy/model/migrate...
migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,170 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
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migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,171 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py...
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migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,171 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py...
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migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,172 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py...
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migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,172 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py...
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migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,172 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py...
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migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,176 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py...
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migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,177 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py...
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migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,178 Loading script lib/galaxy/model/migrate/versions/0026_cloud_tables.py...
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migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,204 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py...
migrate.versioning.script.base DEBUG 2013-12-19 12:18:18,204 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully
migrate.versioning.repository DEBUG 2013-12-19 12:18:18,204 Repository lib/galaxy/model/migrate loaded successfully
migrate.versioning.repository DEBUG 2013-12-19 12:18:18,204 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}}
galaxy.model.migrate.check DEBUG 2013-12-19 12:18:18,212 pysqlite>=2 egg successfully loaded for sqlite dialect
galaxy.model.migrate.check INFO 2013-12-19 12:18:18,262 No database, initializing
galaxy.model.migrate.check INFO 2013-12-19 12:18:18,386 Migrating 0 -> 1...
galaxy.model.migrate.check INFO 2013-12-19 12:18:21,265
galaxy.model.migrate.check INFO 2013-12-19 12:18:21,266 Migrating 1 -> 2...
galaxy.model.migrate.check INFO 2013-12-19 12:18:21,675
galaxy.model.migrate.check INFO 2013-12-19 12:18:21,675 Migrating 2 -> 3...
galaxy.model.migrate.check INFO 2013-12-19 12:18:28,412
galaxy.model.migrate.check INFO 2013-12-19 12:18:28,413 Migrating 3 -> 4...
galaxy.model.migrate.check INFO 2013-12-19 12:18:29,274
galaxy.model.migrate.check INFO 2013-12-19 12:18:29,275 Migrating 4 -> 5...
galaxy.model.custom_types DEBUG 2013-12-19 12:18:29,356 Fixing a discrepancy concerning deleted shared history items.
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py:215: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
galaxy.model.custom_types DEBUG 2013-12-19 12:18:29,432 0 items affected, and restored.
galaxy.model.custom_types DEBUG 2013-12-19 12:18:29,432 Time elapsed: 0.0762670040131
galaxy.model.custom_types DEBUG 2013-12-19 12:18:29,432 Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs.
galaxy.model.custom_types DEBUG 2013-12-19 12:18:29,439 0 items affected, and restored.
galaxy.model.custom_types DEBUG 2013-12-19 12:18:29,440 Time elapsed: 0.00718593597412
galaxy.model.migrate.check INFO 2013-12-19 12:18:29,476
galaxy.model.migrate.check INFO 2013-12-19 12:18:29,476 Migrating 5 -> 6...
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,073 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,073 This migration script changes certain values in the history_dataset_association.extension
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,074 column, specifically 'qual' is chaged to be 'qual454'.
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,074 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,074
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,075 Migrating 6 -> 7...
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,792 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,792 This migration script creates the new history_user_share_association table, and adds
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,793 a new boolean type column to the history table.  This provides support for sharing
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,793 histories in the same way that workflows are shared.
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,793 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,793
galaxy.model.migrate.check INFO 2013-12-19 12:18:30,794 Migrating 7 -> 8...
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,907 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,907 This migration script adds the following new tables for supporting Galaxy forms:
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,908 1) form_definition_current
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,908 2) form_definition
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,908 3) form_values
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,908 4) request_type
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,909 5) request
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,909 6) sample
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,909 7) sample_state
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,909 8) sample_event
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,909 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,910
galaxy.model.migrate.check INFO 2013-12-19 12:18:32,910 Migrating 8 -> 9...
galaxy.model.migrate.check INFO 2013-12-19 12:18:33,645 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:33,646 This migration script adds a new column to 2 tables:
galaxy.model.migrate.check INFO 2013-12-19 12:18:33,646 1) a new boolean type column named 'submitted' to the 'request' table
galaxy.model.migrate.check INFO 2013-12-19 12:18:33,646 2) a new string type column named 'bar_code' to the 'sample' table
galaxy.model.migrate.check INFO 2013-12-19 12:18:33,647 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:33,647
galaxy.model.migrate.check INFO 2013-12-19 12:18:33,647 Migrating 9 -> 10...
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,430 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,431 This migration script adds the history_dataset_association_display_at_authorization table, which
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,431 allows 'private' datasets to be displayed at external sites without making them public.
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,431
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,432 If using mysql, this script will display the following error, which is corrected in the next migration
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,432 script: history_dataset_association_display_at_authorization table failed:  (OperationalError)
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,432 (1059, 'Identifier name  'ix_history_dataset_association_display_at_authorization_update_time'
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,432 is too long.
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,432 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,433
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,433 Migrating 10 -> 11...
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,502 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,503 This script fixes a problem introduced in the previous migration script ( 9->10 ).  MySQL
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,503 has a name length limit and thus the index 'ix_hdadaa_history_dataset_association_id' has
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,503 to be manually created.
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,503 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,504
galaxy.model.migrate.check INFO 2013-12-19 12:18:34,504 Migrating 11 -> 12...
galaxy.model.migrate.check INFO 2013-12-19 12:18:35,500 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:35,501 This script adds a new user_address table that is currently only used with sample requests, where
galaxy.model.migrate.check INFO 2013-12-19 12:18:35,501 a user can select from a list of his addresses to associate with the request.  This script also
galaxy.model.migrate.check INFO 2013-12-19 12:18:35,501 drops the request.submitted column which was boolean and replaces it with a request.state column
galaxy.model.migrate.check INFO 2013-12-19 12:18:35,502 which is a string, allowing for more flexibility with request states.
galaxy.model.migrate.check INFO 2013-12-19 12:18:35,502 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:35,502
galaxy.model.migrate.check INFO 2013-12-19 12:18:35,502 Migrating 12 -> 13...
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,234 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,235 This migration script eliminates all of the tables that were used for the 1st version of the
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,235 library templates where template fields and contents were each stored as a separate table row
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,235 in various library item tables.  All of these tables are dropped in this script, eliminating all
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,236 existing template data.  A total of 14 existing tables are dropped.
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,236
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,236 We're now basing library templates on Galaxy forms, so field contents are stored as a jsonified
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,236 list in the form_values table.  This script introduces the following 3 new association tables:
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,237 1) library_info_association
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,237 2) library_folder_info_association
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,237 3) library_dataset_dataset_info_association
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,237
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,237 If using mysql, this script will throw an (OperationalError) exception due to a long index name
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,238 on the library_dataset_dataset_info_association table, which is OK because the script creates
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,238 an index with a shortened name.
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,238 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,238
galaxy.model.migrate.check INFO 2013-12-19 12:18:37,238 Migrating 13 -> 14...
galaxy.model.migrate.check INFO 2013-12-19 12:18:38,373
galaxy.model.migrate.check INFO 2013-12-19 12:18:38,373 Migration script to add support for "Pages".
galaxy.model.migrate.check INFO 2013-12-19 12:18:38,373   1) Creates Page and PageRevision tables
galaxy.model.migrate.check INFO 2013-12-19 12:18:38,374   2) Adds username column to User table
galaxy.model.migrate.check INFO 2013-12-19 12:18:38,374
galaxy.model.migrate.check INFO 2013-12-19 12:18:38,374
galaxy.model.migrate.check INFO 2013-12-19 12:18:38,374 Migrating 14 -> 15...
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,607
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,608 This migration script adds the tables necessary to support tagging of histories,
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,608 datasets, and history-dataset associations (user views of datasets).
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,608
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,608 If using mysql, this script will display the following error, which is
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,609 corrected in the next migration script:
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,609 history_dataset_association_tag_association table failed:
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,609 (OperationalError) (1059, 'Identifier name
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,609 'ix_history_dataset_association_tag_association_history_dataset_association_id'
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,610 is too long)
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,610
galaxy.model.migrate.check INFO 2013-12-19 12:18:39,610 Migrating 15 -> 16...
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,190
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,190 This script fixes a problem introduced in 0015_tagging.py.  MySQL has a
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,191 name length limit and thus the index 'ix_hda_ta_history_dataset_association_id'
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,191 has to be manually created.
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,191
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,191 Migrating 16 -> 17...
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,877 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,877 This script adds 3 indexes to table columns: library_folder.name,
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,878 library_dataset.name, library_dataset_dataset_association.name.
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,878 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,878
galaxy.model.migrate.check INFO 2013-12-19 12:18:40,878 Migrating 17 -> 18...
galaxy.model.migrate.check INFO 2013-12-19 12:18:42,534
galaxy.model.migrate.check INFO 2013-12-19 12:18:42,534 This migration script provides support for (a) ordering tags by recency and
galaxy.model.migrate.check INFO 2013-12-19 12:18:42,534 (b) tagging pages. This script deletes all existing tags.
galaxy.model.migrate.check INFO 2013-12-19 12:18:42,535
galaxy.model.migrate.check INFO 2013-12-19 12:18:42,535 Migrating 18 -> 19...
galaxy.model.migrate.check INFO 2013-12-19 12:18:43,332 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:43,333 This script creates a request.folder_id column which is a foreign
galaxy.model.migrate.check INFO 2013-12-19 12:18:43,333 key to the library_folder table. This also adds a 'type' and 'layout' column
galaxy.model.migrate.check INFO 2013-12-19 12:18:43,333 to the form_definition table.
galaxy.model.migrate.check INFO 2013-12-19 12:18:43,333 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:43,334
galaxy.model.migrate.check INFO 2013-12-19 12:18:43,334 Migrating 19 -> 20...
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,189
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,189 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,189 This script creates a job_to_output_library_dataset table for allowing library
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,190 uploads to run as regular jobs.  To support this, a library_folder_id column is
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,190 added to the job table, and library_folder/output_library_datasets relations
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,190 are added to the Job object.  An index is also added to the dataset.state
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,190 column.
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,191 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,191
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,191 Migrating 20 -> 21...
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,914
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,914 This migration script adds a user preferences table to Galaxy.
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,914
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,915
galaxy.model.migrate.check INFO 2013-12-19 12:18:44,915 Migrating 21 -> 22...
galaxy.model.migrate.check INFO 2013-12-19 12:18:45,732
galaxy.model.migrate.check INFO 2013-12-19 12:18:45,733 Migration script to add support for storing visualizations.
galaxy.model.migrate.check INFO 2013-12-19 12:18:45,733   1) Creates Visualization and VisualizationRevision tables
galaxy.model.migrate.check INFO 2013-12-19 12:18:45,733
galaxy.model.migrate.check INFO 2013-12-19 12:18:45,733
galaxy.model.migrate.check INFO 2013-12-19 12:18:45,734 Migrating 22 -> 23...
galaxy.model.migrate.check INFO 2013-12-19 12:18:46,958
galaxy.model.migrate.check INFO 2013-12-19 12:18:46,959 Migration script to add columns for tracking whether pages are deleted and
galaxy.model.migrate.check INFO 2013-12-19 12:18:46,960 publicly accessible.
galaxy.model.migrate.check INFO 2013-12-19 12:18:46,960
galaxy.model.migrate.check INFO 2013-12-19 12:18:46,960
galaxy.model.migrate.check INFO 2013-12-19 12:18:46,960 Migrating 23 -> 24...
galaxy.model.migrate.check INFO 2013-12-19 12:18:47,670
galaxy.model.migrate.check INFO 2013-12-19 12:18:47,671 Remove unique constraint from page slugs to allow creating a page with
galaxy.model.migrate.check INFO 2013-12-19 12:18:47,671 the same slug as a deleted page.
galaxy.model.migrate.check INFO 2013-12-19 12:18:47,671
galaxy.model.migrate.check INFO 2013-12-19 12:18:47,671
galaxy.model.migrate.check INFO 2013-12-19 12:18:47,672 Migrating 24 -> 25...
galaxy.model.migrate.check INFO 2013-12-19 12:18:48,391 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:48,392 This script adds a foreign key to the form_values table in the galaxy_user table
galaxy.model.migrate.check INFO 2013-12-19 12:18:48,392 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:48,392
galaxy.model.migrate.check INFO 2013-12-19 12:18:48,393 Migrating 25 -> 26...
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,053
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,054 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,054 This script adds tables needed for Galaxy cloud functionality.
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,055 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,055
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,055 Migrating 26 -> 27...
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,916 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,916 This migration script adds the request_event table and
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,917 removes the state field in the request table
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,917 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,917
galaxy.model.migrate.check INFO 2013-12-19 12:18:50,918 Migrating 27 -> 28...
galaxy.model.migrate.check INFO 2013-12-19 12:18:51,671 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:51,672 This script adds the filename_override_metadata column to the JobExternalOutputMetadata table,
galaxy.model.migrate.check INFO 2013-12-19 12:18:51,672  allowing existing metadata files to be written when using external metadata and a cluster
galaxy.model.migrate.check INFO 2013-12-19 12:18:51,673 set up with read-only access to database/files
galaxy.model.migrate.check INFO 2013-12-19 12:18:51,673 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:18:51,673
galaxy.model.migrate.check INFO 2013-12-19 12:18:51,673 Migrating 28 -> 29...
galaxy.model.migrate.check INFO 2013-12-19 12:18:52,565
galaxy.model.migrate.check INFO 2013-12-19 12:18:52,565 This migration script adds a user actions table to Galaxy.
galaxy.model.migrate.check INFO 2013-12-19 12:18:52,566
galaxy.model.migrate.check INFO 2013-12-19 12:18:52,566
galaxy.model.migrate.check INFO 2013-12-19 12:18:52,566 Migrating 29 -> 30...
galaxy.model.migrate.check INFO 2013-12-19 12:18:53,403
galaxy.model.migrate.check INFO 2013-12-19 12:18:53,404 Migration script to add column for a history slug.
galaxy.model.migrate.check INFO 2013-12-19 12:18:53,404
galaxy.model.migrate.check INFO 2013-12-19 12:18:53,404
galaxy.model.migrate.check INFO 2013-12-19 12:18:53,405 Migrating 30 -> 31...
galaxy.model.migrate.check INFO 2013-12-19 12:18:55,516
galaxy.model.migrate.check INFO 2013-12-19 12:18:55,516 Migration script to (a) add and populate necessary columns for doing community tagging of histories, datasets, and pages and (b) add table for doing individual and community tagging of workflows.
galaxy.model.migrate.check INFO 2013-12-19 12:18:55,517
galaxy.model.migrate.check INFO 2013-12-19 12:18:55,517 SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so this script will generate error messages when run against SQLite; however, script does execute successfully against SQLite.
galaxy.model.migrate.check INFO 2013-12-19 12:18:55,517
galaxy.model.migrate.check INFO 2013-12-19 12:18:55,517
galaxy.model.migrate.check INFO 2013-12-19 12:18:55,518 Migrating 31 -> 32...
galaxy.model.migrate.check INFO 2013-12-19 12:18:56,366
galaxy.model.migrate.check INFO 2013-12-19 12:18:56,366 Migration script to add slug column for stored workflow.
galaxy.model.migrate.check INFO 2013-12-19 12:18:56,367
galaxy.model.migrate.check INFO 2013-12-19 12:18:56,367
galaxy.model.migrate.check INFO 2013-12-19 12:18:56,367 Migrating 32 -> 33...
galaxy.model.migrate.check INFO 2013-12-19 12:18:57,520
galaxy.model.migrate.check INFO 2013-12-19 12:18:57,521 Migration script to add necessary columns for distinguishing between viewing/importing and publishing histories, workflows, and pages. Script adds published column to histories and workflows and importable column to pages.
galaxy.model.migrate.check INFO 2013-12-19 12:18:57,521
galaxy.model.migrate.check INFO 2013-12-19 12:18:57,521
galaxy.model.migrate.check INFO 2013-12-19 12:18:57,521 Migrating 33 -> 34...
galaxy.model.migrate.check INFO 2013-12-19 12:18:58,438
galaxy.model.migrate.check INFO 2013-12-19 12:18:58,439 Migration script to create a table for page-user share association.
galaxy.model.migrate.check INFO 2013-12-19 12:18:58,439
galaxy.model.migrate.check INFO 2013-12-19 12:18:58,440
galaxy.model.migrate.check INFO 2013-12-19 12:18:58,440 Migrating 34 -> 35...
galaxy.model.migrate.check INFO 2013-12-19 12:19:00,451
galaxy.model.migrate.check INFO 2013-12-19 12:19:00,452 Migration script to (a) create tables for annotating objects and (b) create tags for workflow steps.
galaxy.model.migrate.check INFO 2013-12-19 12:19:00,453
galaxy.model.migrate.check INFO 2013-12-19 12:19:00,453
galaxy.model.migrate.check INFO 2013-12-19 12:19:00,453 Migrating 35 -> 36...
galaxy.model.migrate.check INFO 2013-12-19 12:19:01,729
galaxy.model.migrate.check INFO 2013-12-19 12:19:01,730 Migration script to add a deleted column to the following tables:
galaxy.model.migrate.check INFO 2013-12-19 12:19:01,730 library_info_association, library_folder_info_association, library_dataset_dataset_info_association.
galaxy.model.migrate.check INFO 2013-12-19 12:19:01,731
galaxy.model.migrate.check INFO 2013-12-19 12:19:01,731
galaxy.model.migrate.check INFO 2013-12-19 12:19:01,731 Migrating 36 -> 37...
galaxy.model.migrate.check INFO 2013-12-19 12:19:03,866
galaxy.model.migrate.check INFO 2013-12-19 12:19:03,867 This migration script removes the library_id & folder_id fields in the 'request' table and
galaxy.model.migrate.check INFO 2013-12-19 12:19:03,867 adds the same to the 'sample' table. This also adds a 'datatx' column to request_type table
galaxy.model.migrate.check INFO 2013-12-19 12:19:03,868 to store the sequencer login information. Finally, this adds a 'dataset_files' column to
galaxy.model.migrate.check INFO 2013-12-19 12:19:03,868 the sample table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:03,868
galaxy.model.migrate.check INFO 2013-12-19 12:19:03,868
galaxy.model.migrate.check INFO 2013-12-19 12:19:03,869 Migrating 37 -> 38...
galaxy.model.migrate.check INFO 2013-12-19 12:19:05,063
galaxy.model.migrate.check INFO 2013-12-19 12:19:05,063 Migration script to add an inheritable column to the following tables:
galaxy.model.migrate.check INFO 2013-12-19 12:19:05,063 library_info_association, library_folder_info_association.
galaxy.model.migrate.check INFO 2013-12-19 12:19:05,064 Also, in case of sqlite check if the previous migration script deleted the
galaxy.model.migrate.check INFO 2013-12-19 12:19:05,064 request table and if so, restore the table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:05,064
galaxy.model.migrate.check INFO 2013-12-19 12:19:05,064
galaxy.model.migrate.check INFO 2013-12-19 12:19:05,065 Migrating 38 -> 39...
galaxy.model.migrate.check INFO 2013-12-19 12:19:06,014
galaxy.model.migrate.check INFO 2013-12-19 12:19:06,015 Migration script to add a synopsis column to the library table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:06,015
galaxy.model.migrate.check INFO 2013-12-19 12:19:06,016
galaxy.model.migrate.check INFO 2013-12-19 12:19:06,016 Migrating 39 -> 40...
galaxy.model.migrate.check INFO 2013-12-19 12:19:07,113
galaxy.model.migrate.check INFO 2013-12-19 12:19:07,113 Migration script to (a) create tables for annotating pages.
galaxy.model.migrate.check INFO 2013-12-19 12:19:07,114
galaxy.model.migrate.check INFO 2013-12-19 12:19:07,114
galaxy.model.migrate.check INFO 2013-12-19 12:19:07,114 Migrating 40 -> 41...
galaxy.model.migrate.check INFO 2013-12-19 12:19:08,341
galaxy.model.migrate.check INFO 2013-12-19 12:19:08,342 Migration script to create tables for tracking workflow invocations.
galaxy.model.migrate.check INFO 2013-12-19 12:19:08,342
galaxy.model.migrate.check INFO 2013-12-19 12:19:08,342
galaxy.model.migrate.check INFO 2013-12-19 12:19:08,343 Migrating 41 -> 42...
galaxy.model.migrate.check INFO 2013-12-19 12:19:09,634
galaxy.model.migrate.check INFO 2013-12-19 12:19:09,634 Drop and readd workflow invocation tables, allowing null jobs
galaxy.model.migrate.check INFO 2013-12-19 12:19:09,635
galaxy.model.migrate.check INFO 2013-12-19 12:19:09,635
galaxy.model.migrate.check INFO 2013-12-19 12:19:09,635 Migrating 42 -> 43...
galaxy.model.migrate.check INFO 2013-12-19 12:19:11,780
galaxy.model.migrate.check INFO 2013-12-19 12:19:11,781 Migration script to create tables and columns for sharing visualizations.
galaxy.model.migrate.check INFO 2013-12-19 12:19:11,782
galaxy.model.migrate.check INFO 2013-12-19 12:19:11,782
galaxy.model.migrate.check INFO 2013-12-19 12:19:11,782 Migrating 43 -> 44...
galaxy.model.migrate.check INFO 2013-12-19 12:19:13,517
galaxy.model.migrate.check INFO 2013-12-19 12:19:13,518 Migration script to add a notify column to the request table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:13,518
galaxy.model.migrate.check INFO 2013-12-19 12:19:13,519
galaxy.model.migrate.check INFO 2013-12-19 12:19:13,519 Migrating 44 -> 45...
galaxy.model.migrate.check INFO 2013-12-19 12:19:14,658
galaxy.model.migrate.check INFO 2013-12-19 12:19:14,658 Migration script to add the request_type_permissions table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:14,659
galaxy.model.migrate.check INFO 2013-12-19 12:19:14,659
galaxy.model.migrate.check INFO 2013-12-19 12:19:14,659 Migrating 45 -> 46...
galaxy.model.migrate.check INFO 2013-12-19 12:19:15,807
galaxy.model.migrate.check INFO 2013-12-19 12:19:15,808 Migration script to create tables for handling post-job actions.
galaxy.model.migrate.check INFO 2013-12-19 12:19:15,808
galaxy.model.migrate.check INFO 2013-12-19 12:19:15,809
galaxy.model.migrate.check INFO 2013-12-19 12:19:15,809 Migrating 46 -> 47...
galaxy.model.migrate.check INFO 2013-12-19 12:19:16,898
galaxy.model.migrate.check INFO 2013-12-19 12:19:16,898 Add a user_id column to the job table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:16,898
galaxy.model.migrate.check INFO 2013-12-19 12:19:16,899 Updating user_id column in job table for  0  rows...
galaxy.model.migrate.check INFO 2013-12-19 12:19:16,899
galaxy.model.migrate.check INFO 2013-12-19 12:19:16,899 Updated the user_id column for  0  rows in the job table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:16,899 0  rows have no user_id since the value was NULL in the galaxy_session table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:16,900
galaxy.model.migrate.check INFO 2013-12-19 12:19:16,900
galaxy.model.migrate.check INFO 2013-12-19 12:19:16,900 Migrating 47 -> 48...
galaxy.model.migrate.check INFO 2013-12-19 12:19:18,149
galaxy.model.migrate.check INFO 2013-12-19 12:19:18,150 Add a state column to the history_dataset_association and library_dataset_dataset_association table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:18,150
galaxy.model.migrate.check INFO 2013-12-19 12:19:18,150
galaxy.model.migrate.check INFO 2013-12-19 12:19:18,150 Migrating 48 -> 49...
galaxy.model.migrate.check INFO 2013-12-19 12:19:19,321
galaxy.model.migrate.check INFO 2013-12-19 12:19:19,322 Migration script to add the api_keys table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:19,322
galaxy.model.migrate.check INFO 2013-12-19 12:19:19,322
galaxy.model.migrate.check INFO 2013-12-19 12:19:19,323 Migrating 49 -> 50...
galaxy.model.migrate.check INFO 2013-12-19 12:19:21,471
galaxy.model.migrate.check INFO 2013-12-19 12:19:21,472 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:19:21,472 This script drops tables that were associated with the old Galaxy Cloud functionality.
galaxy.model.migrate.check INFO 2013-12-19 12:19:21,472 ========================================
galaxy.model.migrate.check INFO 2013-12-19 12:19:21,473
galaxy.model.migrate.check INFO 2013-12-19 12:19:21,473 Migrating 50 -> 51...
galaxy.model.migrate.check INFO 2013-12-19 12:19:22,545
galaxy.model.migrate.check INFO 2013-12-19 12:19:22,546 Migration script to add imported column for jobs table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:22,546
galaxy.model.migrate.check INFO 2013-12-19 12:19:22,546
galaxy.model.migrate.check INFO 2013-12-19 12:19:22,546 Migrating 51 -> 52...
galaxy.model.migrate.check INFO 2013-12-19 12:19:24,274
galaxy.model.migrate.check INFO 2013-12-19 12:19:24,274 Migration script to add the sample_dataset table and remove the 'dataset_files' column
galaxy.model.migrate.check INFO 2013-12-19 12:19:24,275 from the 'sample' table
galaxy.model.migrate.check INFO 2013-12-19 12:19:24,275
galaxy.model.migrate.check INFO 2013-12-19 12:19:24,275
galaxy.model.migrate.check INFO 2013-12-19 12:19:24,276 Migrating 52 -> 53...
galaxy.model.migrate.check INFO 2013-12-19 12:19:26,173
galaxy.model.migrate.check INFO 2013-12-19 12:19:26,174 Migration script to create tables for rating histories, datasets, workflows, pages, and visualizations.
galaxy.model.migrate.check INFO 2013-12-19 12:19:26,174
galaxy.model.migrate.check INFO 2013-12-19 12:19:26,175
galaxy.model.migrate.check INFO 2013-12-19 12:19:26,175 Migrating 53 -> 54...
galaxy.model.migrate.check INFO 2013-12-19 12:19:27,455
galaxy.model.migrate.check INFO 2013-12-19 12:19:27,455 Migration script to add dbkey column for visualization.
galaxy.model.migrate.check INFO 2013-12-19 12:19:27,456
galaxy.model.migrate.check INFO 2013-12-19 12:19:27,456
galaxy.model.migrate.check INFO 2013-12-19 12:19:27,456 Migrating 54 -> 55...
galaxy.model.migrate.check INFO 2013-12-19 12:19:28,668
galaxy.model.migrate.check INFO 2013-12-19 12:19:28,669 Migration script to add the post_job_action_association table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:28,669
galaxy.model.migrate.check INFO 2013-12-19 12:19:28,669
galaxy.model.migrate.check INFO 2013-12-19 12:19:28,670 Migrating 55 -> 56...
galaxy.model.migrate.check INFO 2013-12-19 12:19:30,685
galaxy.model.migrate.check INFO 2013-12-19 12:19:30,686 Migration script to create tables for adding explicit workflow outputs.
galaxy.model.migrate.check INFO 2013-12-19 12:19:30,686
galaxy.model.migrate.check INFO 2013-12-19 12:19:30,686
galaxy.model.migrate.check INFO 2013-12-19 12:19:30,686 Migrating 56 -> 57...
galaxy.model.migrate.check INFO 2013-12-19 12:19:31,840
galaxy.model.migrate.check INFO 2013-12-19 12:19:31,841 Migration script to modify the 'notify' field in the 'request' table from a boolean
galaxy.model.migrate.check INFO 2013-12-19 12:19:31,841 to a JSONType
galaxy.model.migrate.check INFO 2013-12-19 12:19:31,841
galaxy.model.migrate.check INFO 2013-12-19 12:19:31,842
galaxy.model.migrate.check INFO 2013-12-19 12:19:31,842 Migrating 57 -> 58...
galaxy.model.migrate.check INFO 2013-12-19 12:19:33,209
galaxy.model.migrate.check INFO 2013-12-19 12:19:33,210 Migration script to create table for exporting histories to archives.
galaxy.model.migrate.check INFO 2013-12-19 12:19:33,210
galaxy.model.migrate.check INFO 2013-12-19 12:19:33,210
galaxy.model.migrate.check INFO 2013-12-19 12:19:33,211 Migrating 58 -> 59...
galaxy.model.migrate.check INFO 2013-12-19 12:19:34,635
galaxy.model.migrate.check INFO 2013-12-19 12:19:34,636 Migration script to modify the 'file_path' field type in 'sample_dataset' table
galaxy.model.migrate.check INFO 2013-12-19 12:19:34,636 to 'TEXT' so that it can support large file paths exceeding 255 characters
galaxy.model.migrate.check INFO 2013-12-19 12:19:34,636
galaxy.model.migrate.check INFO 2013-12-19 12:19:34,637
galaxy.model.migrate.check INFO 2013-12-19 12:19:34,637 Migrating 59 -> 60...
galaxy.model.migrate.check INFO 2013-12-19 12:19:36,079
galaxy.model.migrate.check INFO 2013-12-19 12:19:36,079 Migration script to create column and table for importing histories from
galaxy.model.migrate.check INFO 2013-12-19 12:19:36,080 file archives.
galaxy.model.migrate.check INFO 2013-12-19 12:19:36,080
galaxy.model.migrate.check INFO 2013-12-19 12:19:36,080
galaxy.model.migrate.check INFO 2013-12-19 12:19:36,080 Migrating 60 -> 61...
galaxy.model.migrate.check INFO 2013-12-19 12:19:37,398
galaxy.model.migrate.check INFO 2013-12-19 12:19:37,398 Migration script to create tables task management.
galaxy.model.migrate.check INFO 2013-12-19 12:19:37,398
galaxy.model.migrate.check INFO 2013-12-19 12:19:37,399
galaxy.model.migrate.check INFO 2013-12-19 12:19:37,399 Migrating 61 -> 62...
galaxy.model.migrate.check INFO 2013-12-19 12:19:39,740
galaxy.model.migrate.check INFO 2013-12-19 12:19:39,741 Migration script to create table for associating sessions and users with
galaxy.model.migrate.check INFO 2013-12-19 12:19:39,741 OpenIDs.
galaxy.model.migrate.check INFO 2013-12-19 12:19:39,741
galaxy.model.migrate.check INFO 2013-12-19 12:19:39,741
galaxy.model.migrate.check INFO 2013-12-19 12:19:39,742 Migrating 62 -> 63...
galaxy.model.migrate.check INFO 2013-12-19 12:19:41,105
galaxy.model.migrate.check INFO 2013-12-19 12:19:41,106 Migration script to create a new 'sequencer' table
galaxy.model.migrate.check INFO 2013-12-19 12:19:41,107
galaxy.model.migrate.check INFO 2013-12-19 12:19:41,107
galaxy.model.migrate.check INFO 2013-12-19 12:19:41,107 Migrating 63 -> 64...
galaxy.model.migrate.check INFO 2013-12-19 12:19:42,821
galaxy.model.migrate.check INFO 2013-12-19 12:19:42,822 Migration script to add the run and sample_run_association tables.
galaxy.model.migrate.check INFO 2013-12-19 12:19:42,822
galaxy.model.migrate.check INFO 2013-12-19 12:19:42,822
galaxy.model.migrate.check INFO 2013-12-19 12:19:42,823 Migrating 64 -> 65...
galaxy.model.migrate.check INFO 2013-12-19 12:19:44,084
galaxy.model.migrate.check INFO 2013-12-19 12:19:44,085 Migration script to add 'name' attribute to the JSON dict which describes
galaxy.model.migrate.check INFO 2013-12-19 12:19:44,085 a form definition field and the form values in the database. In the 'form_values'
galaxy.model.migrate.check INFO 2013-12-19 12:19:44,085 table, the 'content' column is now a JSON dict instead of a list.
galaxy.model.migrate.check INFO 2013-12-19 12:19:44,085
galaxy.model.migrate.check INFO 2013-12-19 12:19:44,085
galaxy.model.migrate.check INFO 2013-12-19 12:19:44,085 Migrating 65 -> 66...
galaxy.model.migrate.check INFO 2013-12-19 12:19:45,606
galaxy.model.migrate.check INFO 2013-12-19 12:19:45,607 Migration script to create table for storing deferred job and managed transfer
galaxy.model.migrate.check INFO 2013-12-19 12:19:45,607 information.
galaxy.model.migrate.check INFO 2013-12-19 12:19:45,607
galaxy.model.migrate.check INFO 2013-12-19 12:19:45,607
galaxy.model.migrate.check INFO 2013-12-19 12:19:45,607 Migrating 66 -> 67...
galaxy.model.migrate.check INFO 2013-12-19 12:19:47,800
galaxy.model.migrate.check INFO 2013-12-19 12:19:47,800 Migration script to populate the 'sequencer' table and it is populated using unique
galaxy.model.migrate.check INFO 2013-12-19 12:19:47,800 entries in the 'datatx_info' column in the 'request_type' table. It also deletes the 'datatx_info'
galaxy.model.migrate.check INFO 2013-12-19 12:19:47,800 column in the 'request_type' table and adds a foreign key to the 'sequencer' table. The
galaxy.model.migrate.check INFO 2013-12-19 12:19:47,801 actual contents of the datatx_info column are stored as form_values.
galaxy.model.migrate.check INFO 2013-12-19 12:19:47,801
galaxy.model.migrate.check INFO 2013-12-19 12:19:47,801
galaxy.model.migrate.check INFO 2013-12-19 12:19:47,801 Migrating 67 -> 68...
galaxy.model.migrate.check INFO 2013-12-19 12:19:51,317
galaxy.model.migrate.check INFO 2013-12-19 12:19:51,317 This migration script renames the sequencer table to 'external_service' table and
galaxy.model.migrate.check INFO 2013-12-19 12:19:51,317 creates a association table, 'request_type_external_service_association' and
galaxy.model.migrate.check INFO 2013-12-19 12:19:51,318 populates it. The 'sequencer_id' foreign_key from the 'request_type' table is removed.
galaxy.model.migrate.check INFO 2013-12-19 12:19:51,318 The 'sequencer_type_id' column is renamed to 'external_service_type_id' in the renamed
galaxy.model.migrate.check INFO 2013-12-19 12:19:51,318 table 'external_service'. Finally, adds a foreign key to the external_service table in the
galaxy.model.migrate.check INFO 2013-12-19 12:19:51,318 sample_dataset table and populates it.
galaxy.model.migrate.check INFO 2013-12-19 12:19:51,319
galaxy.model.migrate.check INFO 2013-12-19 12:19:51,319
galaxy.model.migrate.check INFO 2013-12-19 12:19:51,319 Migrating 68 -> 69...
galaxy.model.migrate.check INFO 2013-12-19 12:19:52,625
galaxy.model.migrate.check INFO 2013-12-19 12:19:52,626 Migration script to rename the sequencer information form type to external service information form
galaxy.model.migrate.check INFO 2013-12-19 12:19:52,627
galaxy.model.migrate.check INFO 2013-12-19 12:19:52,627
galaxy.model.migrate.check INFO 2013-12-19 12:19:52,627 Migrating 69 -> 70...
galaxy.model.migrate.check INFO 2013-12-19 12:19:53,971
galaxy.model.migrate.check INFO 2013-12-19 12:19:53,972 Migration script to add 'info' column to the transfer_job table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:53,972
galaxy.model.migrate.check INFO 2013-12-19 12:19:53,973
galaxy.model.migrate.check INFO 2013-12-19 12:19:53,973 Migrating 70 -> 71...
galaxy.model.migrate.check INFO 2013-12-19 12:19:56,037
galaxy.model.migrate.check INFO 2013-12-19 12:19:56,038 Migration script to add 'workflow' and 'history' columns for a sample.
galaxy.model.migrate.check INFO 2013-12-19 12:19:56,038
galaxy.model.migrate.check INFO 2013-12-19 12:19:56,038
galaxy.model.migrate.check INFO 2013-12-19 12:19:56,039 Migrating 71 -> 72...
galaxy.model.migrate.check INFO 2013-12-19 12:19:57,447
galaxy.model.migrate.check INFO 2013-12-19 12:19:57,447 Migration script to add 'pid' and 'socket' columns to the transfer_job table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:57,448
galaxy.model.migrate.check INFO 2013-12-19 12:19:57,448
galaxy.model.migrate.check INFO 2013-12-19 12:19:57,448 Migrating 72 -> 73...
galaxy.model.migrate.check INFO 2013-12-19 12:19:59,961
galaxy.model.migrate.check INFO 2013-12-19 12:19:59,962 Migration script to add 'ldda_parent_id' column to the implicitly_converted_dataset_association table.
galaxy.model.migrate.check INFO 2013-12-19 12:19:59,963
galaxy.model.migrate.check INFO 2013-12-19 12:19:59,963
galaxy.model.migrate.check INFO 2013-12-19 12:19:59,963 Migrating 73 -> 74...
galaxy.model.migrate.check INFO 2013-12-19 12:20:01,422
galaxy.model.migrate.check INFO 2013-12-19 12:20:01,423 Migration script to add 'purged' column to the library_dataset table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:01,423
galaxy.model.migrate.check INFO 2013-12-19 12:20:01,424
galaxy.model.migrate.check INFO 2013-12-19 12:20:01,424 Migrating 74 -> 75...
galaxy.model.migrate.check INFO 2013-12-19 12:20:02,874
galaxy.model.migrate.check INFO 2013-12-19 12:20:02,875 Migration script to add a 'subindex' column to the run table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:02,875
galaxy.model.migrate.check INFO 2013-12-19 12:20:02,876
galaxy.model.migrate.check INFO 2013-12-19 12:20:02,876 Migrating 75 -> 76...
galaxy.model.migrate.check INFO 2013-12-19 12:20:04,177
galaxy.model.migrate.check INFO 2013-12-19 12:20:04,178 This migration script fixes the data corruption caused in the form_values
galaxy.model.migrate.check INFO 2013-12-19 12:20:04,179 table (content json field) by migrate script 65.
galaxy.model.migrate.check INFO 2013-12-19 12:20:04,179
galaxy.model.migrate.check INFO 2013-12-19 12:20:04,179 No corrupted rows found.
galaxy.model.migrate.check INFO 2013-12-19 12:20:04,179
galaxy.model.migrate.check INFO 2013-12-19 12:20:04,180 Migrating 76 -> 77...
galaxy.model.migrate.check INFO 2013-12-19 12:20:05,851
galaxy.model.migrate.check INFO 2013-12-19 12:20:05,852 Migration script to create table for storing tool tag associations.
galaxy.model.migrate.check INFO 2013-12-19 12:20:05,852
galaxy.model.migrate.check INFO 2013-12-19 12:20:05,852
galaxy.model.migrate.check INFO 2013-12-19 12:20:05,853 Migrating 77 -> 78...
galaxy.model.migrate.check INFO 2013-12-19 12:20:07,663
galaxy.model.migrate.check INFO 2013-12-19 12:20:07,664 Migration script to add 'total_size' column to the dataset table, 'purged'
galaxy.model.migrate.check INFO 2013-12-19 12:20:07,664 column to the HDA table, and 'disk_usage' column to the User and GalaxySession
galaxy.model.migrate.check INFO 2013-12-19 12:20:07,665 tables.
galaxy.model.migrate.check INFO 2013-12-19 12:20:07,665
galaxy.model.migrate.check INFO 2013-12-19 12:20:07,665
galaxy.model.migrate.check INFO 2013-12-19 12:20:07,665 Migrating 78 -> 79...
galaxy.model.migrate.check INFO 2013-12-19 12:20:10,384
galaxy.model.migrate.check INFO 2013-12-19 12:20:10,384 Migration script to add the job_to_input_library_dataset table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:10,384
galaxy.model.migrate.check INFO 2013-12-19 12:20:10,384
galaxy.model.migrate.check INFO 2013-12-19 12:20:10,385 Migrating 79 -> 80...
galaxy.model.migrate.check INFO 2013-12-19 12:20:12,397
galaxy.model.migrate.check INFO 2013-12-19 12:20:12,397 Migration script to create tables for disk quotas.
galaxy.model.migrate.check INFO 2013-12-19 12:20:12,397
galaxy.model.migrate.check INFO 2013-12-19 12:20:12,397
galaxy.model.migrate.check INFO 2013-12-19 12:20:12,397 Migrating 80 -> 81...
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/dialects/sqlite/base.py:723: SAWarning: Did not recognize type 'BIGINT' of column 'bytes'
galaxy.model.migrate.check INFO 2013-12-19 12:20:13,893
galaxy.model.migrate.check INFO 2013-12-19 12:20:13,894 Migration script to add a 'tool_version' column to the hda/ldda tables.
galaxy.model.migrate.check INFO 2013-12-19 12:20:13,894
galaxy.model.migrate.check INFO 2013-12-19 12:20:13,894
galaxy.model.migrate.check INFO 2013-12-19 12:20:13,894 Migrating 81 -> 82...
galaxy.model.migrate.check INFO 2013-12-19 12:20:15,601
galaxy.model.migrate.check INFO 2013-12-19 12:20:15,602 Migration script to add the tool_shed_repository table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:15,602
galaxy.model.migrate.check INFO 2013-12-19 12:20:15,603
galaxy.model.migrate.check INFO 2013-12-19 12:20:15,603 Migrating 82 -> 83...
galaxy.model.migrate.check INFO 2013-12-19 12:20:17,549
galaxy.model.migrate.check INFO 2013-12-19 12:20:17,550 Migration script to add 'prepare_input_files_cmd' column to the task table and to rename a column.
galaxy.model.migrate.check INFO 2013-12-19 12:20:17,550
galaxy.model.migrate.check INFO 2013-12-19 12:20:17,550
galaxy.model.migrate.check INFO 2013-12-19 12:20:17,551 Migrating 83 -> 84...
galaxy.model.migrate.check INFO 2013-12-19 12:20:20,436
galaxy.model.migrate.check INFO 2013-12-19 12:20:20,436 Migration script to add 'ldda_id' column to the implicitly_converted_dataset_association table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:20,437
galaxy.model.migrate.check INFO 2013-12-19 12:20:20,437
galaxy.model.migrate.check INFO 2013-12-19 12:20:20,437 Migrating 84 -> 85...
galaxy.model.migrate.check INFO 2013-12-19 12:20:21,944
galaxy.model.migrate.check INFO 2013-12-19 12:20:21,946 Migration script to add 'info' column to the task table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:21,946
galaxy.model.migrate.check INFO 2013-12-19 12:20:21,946
galaxy.model.migrate.check INFO 2013-12-19 12:20:21,946 Migrating 85 -> 86...
galaxy.model.migrate.check INFO 2013-12-19 12:20:23,673
galaxy.model.migrate.check INFO 2013-12-19 12:20:23,674 Migration script to add the metadata, update_available and includes_datatypes columns to the tool_shed_repository table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:23,674
galaxy.model.migrate.check INFO 2013-12-19 12:20:23,674
galaxy.model.migrate.check INFO 2013-12-19 12:20:23,674 Migrating 86 -> 87...
galaxy.model.migrate.check INFO 2013-12-19 12:20:25,254
galaxy.model.migrate.check INFO 2013-12-19 12:20:25,256 Migration script to create the tool_id_guid_map table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:25,256
galaxy.model.migrate.check INFO 2013-12-19 12:20:25,256
galaxy.model.migrate.check INFO 2013-12-19 12:20:25,256 Migrating 87 -> 88...
galaxy.model.migrate.check INFO 2013-12-19 12:20:26,811
galaxy.model.migrate.check INFO 2013-12-19 12:20:26,812 Migration script to add the installed_changeset_revision column to the tool_shed_repository table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:26,813
galaxy.model.migrate.check INFO 2013-12-19 12:20:26,813 Updated the installed_changeset_revision column for  0  rows in the tool_shed_repository table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:26,813
galaxy.model.migrate.check INFO 2013-12-19 12:20:26,814 Migrating 88 -> 89...
galaxy.model.migrate.check INFO 2013-12-19 12:20:30,088
galaxy.model.migrate.check INFO 2013-12-19 12:20:30,089 Migration script to add 'object_store_id' column to various tables
galaxy.model.migrate.check INFO 2013-12-19 12:20:30,089
galaxy.model.migrate.check INFO 2013-12-19 12:20:30,089
galaxy.model.migrate.check INFO 2013-12-19 12:20:30,089 Migrating 89 -> 90...
galaxy.model.migrate.check INFO 2013-12-19 12:20:31,748
galaxy.model.migrate.check INFO 2013-12-19 12:20:31,750 Migration script to add the uninstalled and dist_to_shed columns to the tool_shed_repository table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:31,750
galaxy.model.migrate.check INFO 2013-12-19 12:20:31,750
galaxy.model.migrate.check INFO 2013-12-19 12:20:31,751 Migrating 90 -> 91...
galaxy.model.migrate.check INFO 2013-12-19 12:20:33,601
galaxy.model.migrate.check INFO 2013-12-19 12:20:33,602 Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:33,602
galaxy.model.migrate.check INFO 2013-12-19 12:20:33,602 Added 0 rows to the new tool_version table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:33,602
galaxy.model.migrate.check INFO 2013-12-19 12:20:33,602 Migrating 91 -> 92...
galaxy.model.migrate.check INFO 2013-12-19 12:20:35,227
galaxy.model.migrate.check INFO 2013-12-19 12:20:35,228 Migration script to create the migrate_tools table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:35,229
galaxy.model.migrate.check INFO 2013-12-19 12:20:35,229
galaxy.model.migrate.check INFO 2013-12-19 12:20:35,229 Migrating 92 -> 93...
galaxy.model.migrate.check INFO 2013-12-19 12:20:36,860
galaxy.model.migrate.check INFO 2013-12-19 12:20:36,861 Migration script to create "params" column in job table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:36,861
galaxy.model.migrate.check INFO 2013-12-19 12:20:36,862
galaxy.model.migrate.check INFO 2013-12-19 12:20:36,862 Migrating 93 -> 94...
galaxy.model.migrate.check INFO 2013-12-19 12:20:40,046
galaxy.model.migrate.check INFO 2013-12-19 12:20:40,047 Migration script to create "handler" column in job table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:40,048
galaxy.model.migrate.check INFO 2013-12-19 12:20:40,048
galaxy.model.migrate.check INFO 2013-12-19 12:20:40,048 Migrating 94 -> 95...
galaxy.model.migrate.check INFO 2013-12-19 12:20:41,819
galaxy.model.migrate.check INFO 2013-12-19 12:20:41,820 Migration script to create table for tracking history_dataset_association subsets.
galaxy.model.migrate.check INFO 2013-12-19 12:20:41,820
galaxy.model.migrate.check INFO 2013-12-19 12:20:41,820
galaxy.model.migrate.check INFO 2013-12-19 12:20:41,821 Migrating 95 -> 96...
galaxy.model.migrate.check INFO 2013-12-19 12:20:43,471
galaxy.model.migrate.check INFO 2013-12-19 12:20:43,472 Migration script to add column to openid table for provider.
galaxy.model.migrate.check INFO 2013-12-19 12:20:43,473 Remove any OpenID entries with nonunique GenomeSpace Identifier
galaxy.model.migrate.check INFO 2013-12-19 12:20:43,473
galaxy.model.migrate.check INFO 2013-12-19 12:20:43,473
galaxy.model.migrate.check INFO 2013-12-19 12:20:43,473 Migrating 96 -> 97...
galaxy.model.migrate.check INFO 2013-12-19 12:20:45,089
galaxy.model.migrate.check INFO 2013-12-19 12:20:45,090 Migration script to add the ctx_rev column to the tool_shed_repository table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:45,090
galaxy.model.migrate.check INFO 2013-12-19 12:20:45,090
galaxy.model.migrate.check INFO 2013-12-19 12:20:45,090 Migrating 97 -> 98...
galaxy.model.migrate.check INFO 2013-12-19 12:20:47,041
galaxy.model.migrate.check INFO 2013-12-19 12:20:47,042 Migration script to create the genome_index_tool_data table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:47,042
galaxy.model.migrate.check INFO 2013-12-19 12:20:47,042
galaxy.model.migrate.check INFO 2013-12-19 12:20:47,043 Migrating 98 -> 99...
galaxy.model.migrate.check INFO 2013-12-19 12:20:50,343
galaxy.model.migrate.check INFO 2013-12-19 12:20:50,345 Migration script to add the tool_dependency table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:50,345
galaxy.model.migrate.check INFO 2013-12-19 12:20:50,345
galaxy.model.migrate.check INFO 2013-12-19 12:20:50,345 Migrating 99 -> 100...
galaxy.model.migrate.check INFO 2013-12-19 12:20:51,913
galaxy.model.migrate.check INFO 2013-12-19 12:20:51,913 Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text.
galaxy.model.migrate.check INFO 2013-12-19 12:20:51,914
galaxy.model.migrate.check INFO 2013-12-19 12:20:51,914
galaxy.model.migrate.check INFO 2013-12-19 12:20:51,914 Migrating 100 -> 101...
galaxy.model.migrate.check INFO 2013-12-19 12:20:53,752
galaxy.model.migrate.check INFO 2013-12-19 12:20:53,753 Migration script to drop the installed_changeset_revision column from the tool_dependency table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:53,753
galaxy.model.migrate.check INFO 2013-12-19 12:20:53,753
galaxy.model.migrate.check INFO 2013-12-19 12:20:53,754 Migrating 101 -> 102...
galaxy.model.migrate.check INFO 2013-12-19 12:20:55,444
galaxy.model.migrate.check INFO 2013-12-19 12:20:55,446 Migration script to add status and error_message columns to the tool_dependency table and drop the uninstalled column from the tool_dependency table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:55,446
galaxy.model.migrate.check INFO 2013-12-19 12:20:55,446
galaxy.model.migrate.check INFO 2013-12-19 12:20:55,446 Migrating 102 -> 103...
galaxy.model.migrate.check INFO 2013-12-19 12:20:57,159 Migration script to add status and error_message columns to the tool_shed_repository table.
galaxy.model.migrate.check INFO 2013-12-19 12:20:57,160
galaxy.model.migrate.check INFO 2013-12-19 12:20:57,160 Migrating 103 -> 104...
galaxy.model.migrate.check INFO 2013-12-19 12:20:57,260
galaxy.model.migrate.check INFO 2013-12-19 12:20:57,262 Migrating 104 -> 105...
galaxy.model.migrate.check INFO 2013-12-19 12:21:02,138
galaxy.model.migrate.check INFO 2013-12-19 12:21:02,139 Migration script to add the cleanup_event* tables.
galaxy.model.migrate.check INFO 2013-12-19 12:21:02,139
galaxy.model.migrate.check INFO 2013-12-19 12:21:02,139
galaxy.model.migrate.check INFO 2013-12-19 12:21:02,140 Migrating 105 -> 106...
0106_add_missing_indexes DEBUG 2013-12-19 12:21:03,822 Creating index 'ix_metadata_file_lda_id' on column 'lda_id' in table 'metadata_file'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:03,907 Creating index 'ix_history_importable' on column 'importable' in table 'history'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,016 Creating index 'ix_sample_bar_code' on column 'bar_code' in table 'sample'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,102 Creating index 'ix_request_type_deleted' on column 'deleted' in table 'request_type'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,204 Creating index 'ix_galaxy_user_username' on column 'username' in table 'galaxy_user'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,369 Creating index 'ix_form_definition_type' on column 'type' in table 'form_definition'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,429 Creating index 'ix_form_definition_layout' on column 'layout' in table 'form_definition'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,483 Creating index 'ix_job_library_folder_id' on column 'library_folder_id' in table 'job'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,616 Creating index 'ix_page_published' on column 'published' in table 'page'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,702 Creating index 'ix_page_deleted' on column 'deleted' in table 'page'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,703 Creating index 'ix_galaxy_user_form_values_id' on column 'form_values_id' in table 'galaxy_user'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,755 Creating index 'ix_lia_deleted' on column 'deleted' in table 'library_info_association'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,917 Creating index 'ix_lfia_deleted' on column 'deleted' in table 'library_folder_info_association'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,059 Creating index 'ix_lddia_deleted' on column 'deleted' in table 'library_dataset_dataset_info_association'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,205 Creating index 'ix_sample_library_id' on column 'library_id' in table 'sample'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,206 Creating index 'ix_sample_folder_id' on column 'folder_id' in table 'sample'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,275 Creating index 'ix_lia_inheritable' on column 'inheritable' in table 'library_info_association'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,352 Creating index 'ix_lfia_inheritable' on column 'inheritable' in table 'library_folder_info_association'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,420 Creating index 'ix_job_imported' on column 'imported' in table 'job'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,421 Creating index 'ix_request_notification' on column 'notification' in table 'request'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,543 Creating index 'ix_sd_external_service_id' on column 'external_service_id' in table 'sample_dataset'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,663 Creating index 'ix_icda_ldda_parent_id' on column 'ldda_parent_id' in table 'implicitly_converted_dataset_association'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,822 Creating index 'ix_library_dataset_purged' on column 'purged' in table 'library_dataset'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,915 Creating index 'ix_run_subindex' on column 'subindex' in table 'run'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,978 Creating index 'ix_history_dataset_association_purged' on column 'purged' in table 'history_dataset_association'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,065 Creating index 'ix_galaxy_user_disk_usage' on column 'disk_usage' in table 'galaxy_user'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,066 Creating index 'ix_galaxy_session_disk_usage' on column 'disk_usage' in table 'galaxy_session'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,115 Creating index 'ix_icda_ldda_id' on column 'ldda_id' in table 'implicitly_converted_dataset_association'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,176 Creating index 'ix_tsr_includes_datatypes' on column 'includes_datatypes' in table 'tool_shed_repository'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,336 Creating index 'ix_dataset_object_store_id' on column 'object_store_id' in table 'dataset'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,420 Creating index 'ix_job_object_store_id' on column 'object_store_id' in table 'job'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,421 Creating index 'ix_metadata_file_object_store_id' on column 'object_store_id' in table 'metadata_file'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,421 Creating index 'ix_job_handler' on column 'handler' in table 'job'
0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,421 Creating index 'ix_galaxy_user_email' on column 'email' in table 'galaxy_user'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,554
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,555 Migration script to create missing indexes.  Adding new columns to existing tables via SQLAlchemy does not create the index, even if the column definition includes index=True.
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,555
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,555 0106_add_missing_indexes DEBUG 2013-12-19 12:21:03,822 Creating index 'ix_metadata_file_lda_id' on column 'lda_id' in table 'metadata_file'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,555 0106_add_missing_indexes DEBUG 2013-12-19 12:21:03,822 Creating index 'ix_metadata_file_lda_id' on column 'lda_id' in table 'metadata_file'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,556 0106_add_missing_indexes DEBUG 2013-12-19 12:21:03,907 Creating index 'ix_history_importable' on column 'importable' in table 'history'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,556 0106_add_missing_indexes DEBUG 2013-12-19 12:21:03,907 Creating index 'ix_history_importable' on column 'importable' in table 'history'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,556 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,016 Creating index 'ix_sample_bar_code' on column 'bar_code' in table 'sample'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,556 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,016 Creating index 'ix_sample_bar_code' on column 'bar_code' in table 'sample'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,557 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,102 Creating index 'ix_request_type_deleted' on column 'deleted' in table 'request_type'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,557 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,102 Creating index 'ix_request_type_deleted' on column 'deleted' in table 'request_type'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,557 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,204 Creating index 'ix_galaxy_user_username' on column 'username' in table 'galaxy_user'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,557 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,204 Creating index 'ix_galaxy_user_username' on column 'username' in table 'galaxy_user'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,557 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,369 Creating index 'ix_form_definition_type' on column 'type' in table 'form_definition'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,558 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,369 Creating index 'ix_form_definition_type' on column 'type' in table 'form_definition'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,558 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,429 Creating index 'ix_form_definition_layout' on column 'layout' in table 'form_definition'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,558 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,429 Creating index 'ix_form_definition_layout' on column 'layout' in table 'form_definition'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,558 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,483 Creating index 'ix_job_library_folder_id' on column 'library_folder_id' in table 'job'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,558 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,483 Creating index 'ix_job_library_folder_id' on column 'library_folder_id' in table 'job'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,559 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,616 Creating index 'ix_page_published' on column 'published' in table 'page'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,559 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,616 Creating index 'ix_page_published' on column 'published' in table 'page'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,559 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,702 Creating index 'ix_page_deleted' on column 'deleted' in table 'page'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,559 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,702 Creating index 'ix_page_deleted' on column 'deleted' in table 'page'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,559 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,703 Creating index 'ix_galaxy_user_form_values_id' on column 'form_values_id' in table 'galaxy_user'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,560 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,703 Creating index 'ix_galaxy_user_form_values_id' on column 'form_values_id' in table 'galaxy_user'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,560 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,755 Creating index 'ix_lia_deleted' on column 'deleted' in table 'library_info_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,560 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,755 Creating index 'ix_lia_deleted' on column 'deleted' in table 'library_info_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,560 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,917 Creating index 'ix_lfia_deleted' on column 'deleted' in table 'library_folder_info_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,560 0106_add_missing_indexes DEBUG 2013-12-19 12:21:04,917 Creating index 'ix_lfia_deleted' on column 'deleted' in table 'library_folder_info_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,561 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,059 Creating index 'ix_lddia_deleted' on column 'deleted' in table 'library_dataset_dataset_info_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,561 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,059 Creating index 'ix_lddia_deleted' on column 'deleted' in table 'library_dataset_dataset_info_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,561 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,205 Creating index 'ix_sample_library_id' on column 'library_id' in table 'sample'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,561 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,205 Creating index 'ix_sample_library_id' on column 'library_id' in table 'sample'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,561 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,206 Creating index 'ix_sample_folder_id' on column 'folder_id' in table 'sample'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,562 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,206 Creating index 'ix_sample_folder_id' on column 'folder_id' in table 'sample'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,562 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,275 Creating index 'ix_lia_inheritable' on column 'inheritable' in table 'library_info_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,562 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,275 Creating index 'ix_lia_inheritable' on column 'inheritable' in table 'library_info_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,562 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,352 Creating index 'ix_lfia_inheritable' on column 'inheritable' in table 'library_folder_info_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,562 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,352 Creating index 'ix_lfia_inheritable' on column 'inheritable' in table 'library_folder_info_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,563 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,420 Creating index 'ix_job_imported' on column 'imported' in table 'job'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,563 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,420 Creating index 'ix_job_imported' on column 'imported' in table 'job'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,563 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,421 Creating index 'ix_request_notification' on column 'notification' in table 'request'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,563 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,421 Creating index 'ix_request_notification' on column 'notification' in table 'request'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,563 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,543 Creating index 'ix_sd_external_service_id' on column 'external_service_id' in table 'sample_dataset'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,564 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,543 Creating index 'ix_sd_external_service_id' on column 'external_service_id' in table 'sample_dataset'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,564 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,663 Creating index 'ix_icda_ldda_parent_id' on column 'ldda_parent_id' in table 'implicitly_converted_dataset_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,564 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,663 Creating index 'ix_icda_ldda_parent_id' on column 'ldda_parent_id' in table 'implicitly_converted_dataset_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,564 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,822 Creating index 'ix_library_dataset_purged' on column 'purged' in table 'library_dataset'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,564 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,822 Creating index 'ix_library_dataset_purged' on column 'purged' in table 'library_dataset'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,565 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,915 Creating index 'ix_run_subindex' on column 'subindex' in table 'run'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,565 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,915 Creating index 'ix_run_subindex' on column 'subindex' in table 'run'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,565 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,978 Creating index 'ix_history_dataset_association_purged' on column 'purged' in table 'history_dataset_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,565 0106_add_missing_indexes DEBUG 2013-12-19 12:21:05,978 Creating index 'ix_history_dataset_association_purged' on column 'purged' in table 'history_dataset_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,565 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,065 Creating index 'ix_galaxy_user_disk_usage' on column 'disk_usage' in table 'galaxy_user'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,566 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,065 Creating index 'ix_galaxy_user_disk_usage' on column 'disk_usage' in table 'galaxy_user'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,566 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,066 Creating index 'ix_galaxy_session_disk_usage' on column 'disk_usage' in table 'galaxy_session'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,566 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,066 Creating index 'ix_galaxy_session_disk_usage' on column 'disk_usage' in table 'galaxy_session'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,566 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,115 Creating index 'ix_icda_ldda_id' on column 'ldda_id' in table 'implicitly_converted_dataset_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,566 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,115 Creating index 'ix_icda_ldda_id' on column 'ldda_id' in table 'implicitly_converted_dataset_association'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,567 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,176 Creating index 'ix_tsr_includes_datatypes' on column 'includes_datatypes' in table 'tool_shed_repository'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,567 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,176 Creating index 'ix_tsr_includes_datatypes' on column 'includes_datatypes' in table 'tool_shed_repository'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,567 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,336 Creating index 'ix_dataset_object_store_id' on column 'object_store_id' in table 'dataset'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,567 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,336 Creating index 'ix_dataset_object_store_id' on column 'object_store_id' in table 'dataset'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,567 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,420 Creating index 'ix_job_object_store_id' on column 'object_store_id' in table 'job'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,568 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,420 Creating index 'ix_job_object_store_id' on column 'object_store_id' in table 'job'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,568 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,421 Creating index 'ix_metadata_file_object_store_id' on column 'object_store_id' in table 'metadata_file'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,568 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,421 Creating index 'ix_metadata_file_object_store_id' on column 'object_store_id' in table 'metadata_file'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,568 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,421 Creating index 'ix_job_handler' on column 'handler' in table 'job'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,568 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,421 Creating index 'ix_job_handler' on column 'handler' in table 'job'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,569 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,421 Creating index 'ix_galaxy_user_email' on column 'email' in table 'galaxy_user'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,569 0106_add_missing_indexes DEBUG 2013-12-19 12:21:06,421 Creating index 'ix_galaxy_user_email' on column 'email' in table 'galaxy_user'
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,569
galaxy.model.migrate.check INFO 2013-12-19 12:21:06,569 Migrating 106 -> 107...
galaxy.model.migrate.check INFO 2013-12-19 12:21:08,460
galaxy.model.migrate.check INFO 2013-12-19 12:21:08,461 Add the exit_code column to the Job and Task tables.
galaxy.model.migrate.check INFO 2013-12-19 12:21:08,462
galaxy.model.migrate.check INFO 2013-12-19 12:21:08,462
galaxy.model.migrate.check INFO 2013-12-19 12:21:08,462 Migrating 107 -> 108...
galaxy.model.migrate.check INFO 2013-12-19 12:21:11,240
galaxy.model.migrate.check INFO 2013-12-19 12:21:11,242 Add the ExtendedMetadata and ExtendedMetadataIndex tables
galaxy.model.migrate.check INFO 2013-12-19 12:21:11,242
galaxy.model.migrate.check INFO 2013-12-19 12:21:11,242
galaxy.model.migrate.check INFO 2013-12-19 12:21:11,243 Migrating 108 -> 109...
galaxy.model.migrate.check INFO 2013-12-19 12:21:15,121
galaxy.model.migrate.check INFO 2013-12-19 12:21:15,123 Migration script to add the repository_dependency and repository_repository_dependency_association tables.
galaxy.model.migrate.check INFO 2013-12-19 12:21:15,123
galaxy.model.migrate.check INFO 2013-12-19 12:21:15,123
galaxy.model.migrate.check INFO 2013-12-19 12:21:15,124 Migrating 109 -> 110...
galaxy.model.migrate.check INFO 2013-12-19 12:21:17,009
galaxy.model.migrate.check INFO 2013-12-19 12:21:17,010 Add UUID column to dataset table
galaxy.model.migrate.check INFO 2013-12-19 12:21:17,010
galaxy.model.migrate.check INFO 2013-12-19 12:21:17,010
galaxy.model.migrate.check INFO 2013-12-19 12:21:17,011 Migrating 110 -> 111...
galaxy.model.migrate.check INFO 2013-12-19 12:21:18,994
galaxy.model.migrate.check INFO 2013-12-19 12:21:18,995 Add support for job destinations to the job table
galaxy.model.migrate.check INFO 2013-12-19 12:21:18,995
galaxy.model.migrate.check INFO 2013-12-19 12:21:18,995
galaxy.model.migrate.check INFO 2013-12-19 12:21:18,996 Migrating 111 -> 112...
0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-12-19 12:21:20,974 Created data_manager_history_association table
0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-12-19 12:21:21,201 Created data_manager_job_association table
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,278
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,279 Migration script to add the data_manager_history_association table and data_manager_job_association.
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,279
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,280 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-12-19 12:21:20,974 Created data_manager_history_association table
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,280 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-12-19 12:21:20,974 Created data_manager_history_association table
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,280 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-12-19 12:21:21,201 Created data_manager_job_association table
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,280 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2013-12-19 12:21:21,201 Created data_manager_job_association table
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,281
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,281 Migrating 112 -> 113...
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,409
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,410 Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate.
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,410
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,411
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,411 Migrating 113 -> 114...
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,537
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,538 Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate.
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,538
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,539
galaxy.model.migrate.check INFO 2013-12-19 12:21:21,539 Migrating 114 -> 115...
galaxy.model.migrate.check INFO 2013-12-19 12:21:22,858
galaxy.model.migrate.check INFO 2013-12-19 12:21:22,860 Migrating 115 -> 116...
galaxy.model.migrate.check INFO 2013-12-19 12:21:26,711
galaxy.model.migrate.check INFO 2013-12-19 12:21:26,712 Migration script to drop the update_available Boolean column and replace it with the tool_shed_status JSONType column in the tool_shed_repository table.
galaxy.model.migrate.check INFO 2013-12-19 12:21:26,713
galaxy.model.migrate.check INFO 2013-12-19 12:21:26,713
galaxy.model.migrate.check INFO 2013-12-19 12:21:26,713 Migrating 116 -> 117...
galaxy.model.migrate.check INFO 2013-12-19 12:21:28,738
galaxy.model.migrate.check INFO 2013-12-19 12:21:28,740 Created on Sep 10, 2013
galaxy.model.migrate.check INFO 2013-12-19 12:21:28,740
galaxy.model.migrate.check INFO 2013-12-19 12:21:28,741 @author: marten
galaxy.model.migrate.check INFO 2013-12-19 12:21:28,741
galaxy.model.migrate.check INFO 2013-12-19 12:21:28,741 Adds 'active' and 'activation_token' columns to the galaxy_user table.
galaxy.model.migrate.check INFO 2013-12-19 12:21:28,741
galaxy.model.migrate.check INFO 2013-12-19 12:21:28,741
migrate.versioning.repository DEBUG 2013-12-19 12:21:28,789 Loading repository lib/tool_shed/galaxy_install/migrate...
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,789 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py...
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,789 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,790 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py...
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,790 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,790 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py...
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,790 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,790 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py...
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,790 Script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,791 Loading script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py...
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,791 Script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,791 Loading script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py...
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,791 Script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,791 Loading script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py...
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,791 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,792 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py...
migrate.versioning.script.base DEBUG 2013-12-19 12:21:28,792 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully
migrate.versioning.repository DEBUG 2013-12-19 12:21:28,792 Repository lib/tool_shed/galaxy_install/migrate loaded successfully
migrate.versioning.repository DEBUG 2013-12-19 12:21:28,792 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_tools', 'repository_id': 'GalaxyTools'}}
tool_shed.galaxy_install.migrate.check DEBUG 2013-12-19 12:21:28,800 pysqlite>=2 egg successfully loaded for sqlite dialect
galaxy.model.mapping DEBUG 2013-12-19 12:21:28,853 pysqlite>=2 egg successfully loaded for sqlite dialect
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,896 Loading datatypes from datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,915 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,915 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,915 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,915 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,916 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,916 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,916 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,916 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,916 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,917 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,917 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,917 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,918 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,918 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,918 Loaded sniffer for datatype 'galaxy.datatypes.images:Html'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,919 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,919 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,919 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,920 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,920 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,920 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,921 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,921 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,921 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,922 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,922 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,922 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,923 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,923 Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,923 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,924 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,924 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,924 Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,925 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,925 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,926 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,926 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,926 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,927 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,927 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,928 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,928 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,928 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2013-12-19 12:21:28,929 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,959 Loaded tool data table 'all_fasta'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,960 Loaded tool data table 'bfast_indexes'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,960 Loaded tool data table 'blastdb'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,960 Loaded tool data table 'blastdb_p'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,961 Loaded tool data table 'bowtie2_indexes'
galaxy.tools.data WARNING 2013-12-19 12:21:28,961 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,961 Loaded tool data table 'bwa_indexes'
galaxy.tools.data WARNING 2013-12-19 12:21:28,962 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,962 Loaded tool data table 'bwa_indexes_color'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,962 Loaded tool data table 'indexed_maf_files'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,962 Loaded tool data table 'ngs_sim_fasta'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,963 Loaded tool data table 'perm_base_indexes'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,963 Loaded tool data table 'perm_color_indexes'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,964 Loaded tool data table 'picard_indexes'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,964 Loaded tool data table 'gatk_picard_indexes'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,964 Loaded tool data table 'gatk_annotations'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,965 Loaded tool data table 'srma_indexes'
galaxy.tools.data WARNING 2013-12-19 12:21:28,965 Cannot find index file 'tool-data/bowtie_indices.loc' for tool data table 'tophat_indexes'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,965 Loaded tool data table 'tophat_indexes'
galaxy.tools.data WARNING 2013-12-19 12:21:28,965 Cannot find index file 'tool-data/bowtie_indices_color.loc' for tool data table 'tophat_indexes_color'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,966 Loaded tool data table 'tophat_indexes_color'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,966 Loaded tool data table 'tophat2_indexes'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,966 Loaded tool data table 'ccat_configurations'
galaxy.tools.data DEBUG 2013-12-19 12:21:28,967 Loaded tool data table 'mosaik_indexes'
galaxy.jobs WARNING 2013-12-19 12:21:28,967 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/tmpAntFXD/functional_tests_wsgi.ini" instead
galaxy.jobs DEBUG 2013-12-19 12:21:28,967 Loading job configuration from /tmp/tmpAntFXD/functional_tests_wsgi.ini
galaxy.jobs DEBUG 2013-12-19 12:21:28,968 Done loading job configuration
galaxy.tools INFO 2013-12-19 12:21:28,984 Parsing the tool configuration ./tool_conf.xml
galaxy.tools WARNING 2013-12-19 12:21:52,047 Tool maximal_information_based_nonparametric_exploration: a when tag has not been defined for 'master_variable_type (master_variable_type_selector) --> allPairs', assuming empty inputs.
galaxy.tools WARNING 2013-12-19 12:22:05,112 Tool fastq_manipulation: a when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable.
docutils WARNING 2013-12-19 12:22:07,910 <string>:50: (WARNING/2) Literal block expected; none found.

galaxy.tools INFO 2013-12-19 12:22:17,389 Parsing the tool configuration ./migrated_tools_conf.xml
galaxy.tools DEBUG 2013-12-19 12:22:17,390 Loading section: Get Data
galaxy.tools DEBUG 2013-12-19 12:22:17,390 Loaded tool id: upload1, version: 1.1.3 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,390 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,390 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,390 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,391 Loaded tool id: bx_browser, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,391 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,391 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,391 Loaded tool id: biomart, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,391 Loaded tool id: biomart_test, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,391 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,392 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,392 Loaded tool id: modENCODEfly, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,392 Loaded tool id: flymine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,392 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,392 Loaded tool id: modmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,392 Loaded tool id: mousemine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,393 Loaded tool id: ratmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,393 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,393 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,393 Loaded tool id: modENCODEworm, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,393 Loaded tool id: wormbase, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,393 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,393 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,394 Loaded tool id: encode_db1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,394 Loaded tool id: epigraph_import, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,394 Loaded tool id: epigraph_import_test, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,394 Loaded tool id: hbvar, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,394 Loaded tool id: genomespace_file_browser_prod, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,394 Loaded tool id: genomespace_importer, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,395 Loaded tool id: fix_errors, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,395 Loading section: Send Data
galaxy.tools DEBUG 2013-12-19 12:22:17,395 Loaded tool id: epigraph_export, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,395 Loaded tool id: epigraph_test_export, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,395 Loaded tool id: genomespace_exporter, version: 0.0.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,395 Loading section: ENCODE Tools
galaxy.tools DEBUG 2013-12-19 12:22:17,396 Loaded tool id: gencode_partition1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,396 Loaded tool id: random_intervals1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,396 Loading section: Lift-Over
galaxy.tools DEBUG 2013-12-19 12:22:17,396 Loaded tool id: liftOver1, version: 1.0.3 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,396 Loading section: Text Manipulation
galaxy.tools DEBUG 2013-12-19 12:22:17,396 Loaded tool id: addValue, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,397 Loaded tool id: Add_a_column1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,397 Loaded tool id: cat1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,397 Loaded tool id: Cut1, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,397 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,397 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,397 Loaded tool id: createInterval, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,397 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,398 Loaded tool id: Paste1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,398 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,398 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,398 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,398 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,398 Loaded tool id: trimmer, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,399 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,399 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,399 Loaded tool id: dna_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,399 Loaded tool id: tables_arithmetic_operations, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,399 Loading section: Filter and Sort
galaxy.tools DEBUG 2013-12-19 12:22:17,399 Loaded tool id: Filter1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,400 Loaded tool id: sort1, version: 1.0.3 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,400 Loaded tool id: Grep1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,400 Loaded label: GFF
galaxy.tools DEBUG 2013-12-19 12:22:17,400 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,400 Loaded tool id: gff_filter_by_attribute, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,400 Loaded tool id: gff_filter_by_feature_count, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,400 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,401 Loading section: Join, Subtract and Group
galaxy.tools DEBUG 2013-12-19 12:22:17,401 Loaded tool id: join1, version: 2.0.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,401 Loaded tool id: comp1, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,401 Loaded tool id: subtract_query1, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,401 Loaded tool id: Grouping1, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,401 Loaded tool id: column_join, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,402 Loading section: Convert Formats
galaxy.tools DEBUG 2013-12-19 12:22:17,402 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,402 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,402 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,402 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,402 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,403 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,403 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,403 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,403 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,403 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,403 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,403 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,404 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,404 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,404 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,404 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,404 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,404 Loading section: Extract Features
galaxy.tools DEBUG 2013-12-19 12:22:17,404 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,405 Loading section: Fetch Sequences
galaxy.tools DEBUG 2013-12-19 12:22:17,405 Loaded tool id: Extract genomic DNA 1, version: 2.2.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,405 Loading section: Fetch Alignments
galaxy.tools DEBUG 2013-12-19 12:22:17,405 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,405 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,405 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,406 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,406 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,406 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,406 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,406 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,406 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,407 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,407 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,407 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,407 Loading section: Get Genomic Scores
galaxy.tools DEBUG 2013-12-19 12:22:17,407 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,407 Loaded tool id: aggregate_scores_in_intervals2, version: 1.1.3 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,408 Loaded tool id: phastOdds_for_intervals, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,408 Loading section: Operate on Genomic Intervals
galaxy.tools DEBUG 2013-12-19 12:22:17,408 Loaded tool id: gops_intersect_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,408 Loaded tool id: gops_subtract_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,408 Loaded tool id: gops_merge_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,408 Loaded tool id: gops_concat_1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,409 Loaded tool id: gops_basecoverage_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,409 Loaded tool id: gops_coverage_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,409 Loaded tool id: gops_complement_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,409 Loaded tool id: gops_cluster_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,409 Loaded tool id: gops_join_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,409 Loaded tool id: get_flanks1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,409 Loaded tool id: flanking_features_1, version: 4.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,410 Loaded tool id: Annotation_Profiler_0, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,410 Loading section: Statistics
galaxy.tools DEBUG 2013-12-19 12:22:17,410 Loaded tool id: Summary_Statistics1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,410 Loaded tool id: Count1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,410 Loaded tool id: cor2, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,410 Loaded tool id: generate_matrix_for_pca_and_lda1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,411 Loaded tool id: lda_analy1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,411 Loaded tool id: plot_for_lda_output1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,411 Loaded tool id: maximal_information_based_nonparametric_exploration, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,411 Loaded label: GFF
galaxy.tools DEBUG 2013-12-19 12:22:17,411 Loaded tool id: count_gff_features, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,411 Loading section: Wavelet Analysis
galaxy.tools DEBUG 2013-12-19 12:22:17,412 Loaded tool id: dwt_var1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,412 Loading section: Graph/Display Data
galaxy.tools DEBUG 2013-12-19 12:22:17,412 Loaded tool id: histogram_rpy, version: 1.0.3 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,412 Loaded tool id: scatterplot_rpy, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,412 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,412 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,413 Loaded tool id: gmaj_1, version: 2.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,413 Loaded tool id: laj_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,413 Loaded tool id: build_ucsc_custom_track_1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,413 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,413 Loaded tool id: mutation_visualize, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,413 Loading section: Regional Variation
galaxy.tools DEBUG 2013-12-19 12:22:17,414 Loaded tool id: winSplitter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,414 Loaded tool id: featureCoverage1, version: 2.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,414 Loaded tool id: wtavg, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,414 Loaded tool id: qualityFilter, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,414 Loaded tool id: cpgFilter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,414 Loaded tool id: getIndels_2way, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,414 Loaded tool id: indelRates_3way, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,415 Loaded tool id: substitutions1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,415 Loaded tool id: subRate1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,415 Loaded tool id: microsats_align1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,415 Loaded tool id: microsats_mutability1, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,415 Loading section: Multiple regression
galaxy.tools DEBUG 2013-12-19 12:22:17,415 Loaded tool id: LinearRegression1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,416 Loaded tool id: LogisticRegression, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,416 Loaded tool id: BestSubsetsRegression1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,416 Loaded tool id: rcve1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,416 Loaded tool id: partialRsq, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,416 Loading section: Multivariate Analysis
galaxy.tools DEBUG 2013-12-19 12:22:17,416 Loaded tool id: pca1, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,417 Loaded tool id: cca1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,417 Loaded tool id: kpca1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,417 Loaded tool id: kcca1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,417 Loading section: Evolution
galaxy.tools DEBUG 2013-12-19 12:22:17,417 Loaded tool id: hyphy_branch_lengths_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,417 Loaded tool id: hyphy_nj_tree_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,418 Loaded tool id: hyphy_dnds_wrapper1, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,418 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,418 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,418 Loading section: Motif Tools
galaxy.tools DEBUG 2013-12-19 12:22:17,418 Loaded tool id: meme_meme, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,418 Loaded tool id: meme_fimo, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,418 Loaded tool id: rgweblogo3, version: 0.4 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,419 Loading section: Multiple Alignments
galaxy.tools DEBUG 2013-12-19 12:22:17,419 Loaded tool id: clustalw, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,419 Loading section: Metagenomic analyses
galaxy.tools DEBUG 2013-12-19 12:22:17,419 Loaded tool id: Fetch Taxonomic Ranks, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,419 Loaded tool id: t2t_report, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,419 Loaded tool id: Draw_phylogram, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,420 Loaded tool id: find_diag_hits, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,420 Loaded tool id: lca1, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,420 Loaded tool id: poisson2test, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,420 Loading section: FASTA manipulation
galaxy.tools DEBUG 2013-12-19 12:22:17,420 Loaded tool id: fasta_compute_length, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,420 Loaded tool id: fasta_filter_by_length, version: 1.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,421 Loaded tool id: fasta_concatenate0, version: 0.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,421 Loaded tool id: fasta2tab, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,421 Loaded tool id: tab2fasta, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,421 Loading section: NGS: QC and manipulation
galaxy.tools DEBUG 2013-12-19 12:22:17,421 Loaded label: FastQC: fastq/sam/bam
galaxy.tools DEBUG 2013-12-19 12:22:17,421 Loaded tool id: fastqc, version: 0.52 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,422 Loaded label: Illumina fastq
galaxy.tools DEBUG 2013-12-19 12:22:17,422 Loaded tool id: fastq_groomer, version: 1.0.4 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,422 Loaded tool id: fastq_paired_end_splitter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,422 Loaded tool id: fastq_paired_end_joiner, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,422 Loaded tool id: fastq_stats, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,422 Loaded label: Roche-454 data
galaxy.tools DEBUG 2013-12-19 12:22:17,422 Loaded tool id: quality_score_distribution, version: 1.0.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,423 Loaded tool id: trim_reads, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,423 Loaded tool id: fastq_combiner, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,423 Loaded label: AB-SOLiD data
galaxy.tools DEBUG 2013-12-19 12:22:17,423 Loaded tool id: solid2fastq, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,423 Loaded tool id: solid_qual_stats, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,423 Loaded tool id: solid_qual_boxplot, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,423 Loaded label: Generic FASTQ manipulation
galaxy.tools DEBUG 2013-12-19 12:22:17,424 Loaded tool id: fastq_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,424 Loaded tool id: fastq_trimmer, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,424 Loaded tool id: fastq_quality_trimmer, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,424 Loaded tool id: fastq_masker_by_quality, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,424 Loaded tool id: fastq_paired_end_interlacer, version: 1.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,424 Loaded tool id: fastq_paired_end_deinterlacer, version: 1.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,425 Loaded tool id: fastq_manipulation, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,425 Loaded tool id: fastq_to_fasta_python, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,425 Loaded tool id: fastq_to_tabular, version: 1.1.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,425 Loaded tool id: tabular_to_fastq, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,425 Loaded label: FASTX-Toolkit for FASTQ data
galaxy.tools DEBUG 2013-12-19 12:22:17,425 Loading section: NGS: Mapping
galaxy.tools DEBUG 2013-12-19 12:22:17,425 Loaded tool id: bowtie2, version: 0.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,426 Loaded tool id: bfast_wrapper, version: 0.1.3 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,426 Loaded tool id: megablast_wrapper, version: 1.2.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,426 Loaded tool id: megablast_xml_parser, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,426 Loaded tool id: PerM, version: 1.1.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,426 Loaded tool id: srma_wrapper, version: 0.2.5 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,426 Loaded tool id: mosaik_wrapper, version: 1.1.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,427 Loading section: NGS: Indel Analysis
galaxy.tools DEBUG 2013-12-19 12:22:17,427 Loaded tool id: sam_indel_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,427 Loaded tool id: indel_table, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,427 Loaded tool id: indel_analysis, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,427 Loading section: NGS: RNA Analysis
galaxy.tools DEBUG 2013-12-19 12:22:17,427 Loaded label: RNA-seq
galaxy.tools DEBUG 2013-12-19 12:22:17,428 Loaded tool id: tophat, version: 1.5.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,428 Loaded tool id: tophat2, version: 0.6 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,428 Loaded tool id: tophat_color, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,428 Loaded tool id: express, version: 1.1.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,428 Loaded label: Filtering
galaxy.tools DEBUG 2013-12-19 12:22:17,428 Loaded tool id: filter_combined_via_tracking, version: 0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,429 Loading section: NGS: SAM Tools
galaxy.tools DEBUG 2013-12-19 12:22:17,429 Loading section: NGS: GATK Tools (beta)
galaxy.tools DEBUG 2013-12-19 12:22:17,429 Loaded label: Alignment Utilities
galaxy.tools DEBUG 2013-12-19 12:22:17,429 Loaded tool id: gatk_depth_of_coverage, version: 0.0.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,429 Loaded tool id: gatk_print_reads, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,429 Loaded label: Realignment
galaxy.tools DEBUG 2013-12-19 12:22:17,429 Loaded tool id: gatk_realigner_target_creator, version: 0.0.4 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,430 Loaded tool id: gatk_indel_realigner, version: 0.0.6 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,430 Loaded label: Base Recalibration
galaxy.tools DEBUG 2013-12-19 12:22:17,430 Loaded tool id: gatk_count_covariates, version: 0.0.5 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,430 Loaded tool id: gatk_table_recalibration, version: 0.0.5 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,430 Loaded tool id: gatk_analyze_covariates, version: 0.0.5 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,430 Loaded label: Genotyping
galaxy.tools DEBUG 2013-12-19 12:22:17,431 Loaded tool id: gatk_unified_genotyper, version: 0.0.6 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,431 Loaded label: Annotation
galaxy.tools DEBUG 2013-12-19 12:22:17,431 Loaded tool id: gatk_variant_annotator, version: 0.0.5 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,431 Loaded label: Filtration
galaxy.tools DEBUG 2013-12-19 12:22:17,431 Loaded tool id: gatk_variant_filtration, version: 0.0.5 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,431 Loaded tool id: gatk_variant_select, version: 0.0.2 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,431 Loaded label: Variant Quality Score Recalibration
galaxy.tools DEBUG 2013-12-19 12:22:17,432 Loaded tool id: gatk_variant_recalibrator, version: 0.0.4 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,432 Loaded tool id: gatk_variant_apply_recalibration, version: 0.0.4 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,432 Loaded label: Variant Utilities
galaxy.tools DEBUG 2013-12-19 12:22:17,432 Loaded tool id: gatk_validate_variants, version: 0.0.4 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,432 Loaded tool id: gatk_variant_eval, version: 0.0.8 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,432 Loaded tool id: gatk_variant_combine, version: 0.0.4 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,432 Loading section: NGS: Peak Calling
galaxy.tools DEBUG 2013-12-19 12:22:17,433 Loaded tool id: peakcalling_macs, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,433 Loaded tool id: peakcalling_sicer, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,433 Loaded tool id: peakcalling_ccat, version: 0.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,433 Loading section: NGS: Simulation
galaxy.tools DEBUG 2013-12-19 12:22:17,433 Loaded tool id: ngs_simulation, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,433 Loading section: Phenotype Association
galaxy.tools DEBUG 2013-12-19 12:22:17,434 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,434 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,434 Loaded tool id: hgv_sift, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,434 Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,434 Loaded tool id: hgv_david, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,434 Loaded tool id: hgv_snpFreq, version: 1.0.1 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,435 Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,435 Loaded tool id: hgv_pass, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,435 Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,435 Loaded tool id: hgv_beam, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,435 Loaded tool id: hgv_lps, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,435 Loaded tool id: freebayes_wrapper, version: 0.5.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,436 Loaded tool id: master2pgSnp, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,436 Loaded tool id: vcf2pgSnp, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,436 Loading section: VCF Tools
galaxy.tools DEBUG 2013-12-19 12:22:17,436 Loaded tool id: vcf_intersect, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,436 Loaded tool id: vcf_annotate, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,436 Loaded tool id: vcf_filter, version: 1.0.0 into tool panel.
galaxy.tools DEBUG 2013-12-19 12:22:17,436 Loaded tool id: vcf_extract, version: 1.0.0 into tool panel.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,599 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,604 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,608 Loaded display application 'igv_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,610 Loaded display application 'igb_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,612 Loaded display application 'igb_bed' for datatype 'bed', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,618 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,620 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,626 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,628 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,640 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,651 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,667 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,669 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,673 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,680 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,684 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,686 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,688 Loaded display application 'igb_wig' for datatype 'wig', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,693 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False.
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,693 Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,693 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,693 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,694 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,694 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,694 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,695 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,695 Adding inherited display application 'ensembl_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,695 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,695 Adding inherited display application 'rviewer_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,696 Adding inherited display application 'ensembl_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,696 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,696 Adding inherited display application 'rviewer_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,697 Adding inherited display application 'ensembl_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,697 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,697 Adding inherited display application 'rviewer_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,698 Adding inherited display application 'ensembl_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,698 Adding inherited display application 'ensembl_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,698 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,698 Adding inherited display application 'rviewer_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,699 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,699 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,699 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,711 Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,724 Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,737 Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,750 Loaded converter: CONVERTER_bed_to_bgzip_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,763 Loaded converter: CONVERTER_bed_to_tabix_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,784 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,797 Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,810 Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,823 Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,836 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,849 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,862 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,875 Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,889 Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,902 Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,916 Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,935 Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,948 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,961 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,974 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:17,987 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:18,000 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:18,013 Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:18,026 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:18,039 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:18,052 Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:18,065 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:18,078 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:18,097 Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,105 Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,118 Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,132 Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,145 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,158 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,172 Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,185 Loaded converter: CONVERTER_picard_interval_list_to_bed6
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,198 Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,212 Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,231 Loaded converter: CONVERTER_encodepeak_to_tabix_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,244 Loaded converter: CONVERTER_encodepeak_to_bgzip_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,258 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,271 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,284 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,297 Loaded converter: CONVERTER_sam_to_bam
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,311 Loaded converter: CONVERTER_sam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,324 Loaded converter: CONVERTER_vcf_to_bgzip_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,337 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,350 Loaded converter: CONVERTER_vcf_to_tabix_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,364 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,377 Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,379 Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,400 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,412 Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,426 Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,439 Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,452 Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2013-12-19 12:22:20,455 Loaded external metadata tool: __SET_METADATA__
galaxy.tools.imp_exp DEBUG 2013-12-19 12:22:20,458 Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.imp_exp DEBUG 2013-12-19 12:22:20,461 Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools.genome_index DEBUG 2013-12-19 12:22:20,463 Loaded genome index tool: __GENOME_INDEX__
galaxy.jobs.manager DEBUG 2013-12-19 12:22:20,464 Starting job handler
galaxy.jobs.runners DEBUG 2013-12-19 12:22:20,465 Starting 5 LocalRunner workers
galaxy.jobs DEBUG 2013-12-19 12:22:20,467 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.runners DEBUG 2013-12-19 12:22:20,478 Starting 3 LWRRunner workers
galaxy.jobs DEBUG 2013-12-19 12:22:20,481 Loaded job runner 'galaxy.jobs.runners.lwr:LwrJobRunner' as 'lwr'
galaxy.jobs DEBUG 2013-12-19 12:22:20,481 Legacy destination with id 'local:///', url 'local:///' converted, got params:
galaxy.jobs.handler DEBUG 2013-12-19 12:22:20,481 Loaded job runners plugins: lwr:local
galaxy.jobs.handler INFO 2013-12-19 12:22:20,482 job handler stop queue started
galaxy.jobs.handler INFO 2013-12-19 12:22:20,503 job handler queue started
galaxy.sample_tracking.external_service_types DEBUG 2013-12-19 12:22:20,507 Loaded external_service_type: Simple unknown sequencer 1.0.0
galaxy.sample_tracking.external_service_types DEBUG 2013-12-19 12:22:20,511 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
functional_tests.py INFO 2013-12-19 12:22:20,511 Embedded Universe application started
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,518 Enabling 'page' controller, class: PageController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,519 Enabling 'root' controller, class: RootController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,880 Enabling 'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,880 Enabling 'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,882 Enabling 'biostar' controller, class: BiostarController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,895 Enabling 'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,895 Enabling 'admin' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,896 Enabling 'mobile' controller, class: Mobile
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,906 Enabling 'data_admin' controller, class: DataAdmin
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,908 Enabling 'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,908 Enabling 'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,910 Enabling 'user' controller, class: User
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,914 Enabling 'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,923 Enabling 'data_manager' controller, class: DataManager
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,923 Enabling 'search' controller, class: SearchController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,924 Enabling 'ucsc_proxy' controller, class: UCSCProxy
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,925 Enabling 'error' controller, class: Error
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,935 Enabling 'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,947 Enabling 'requests_admin' controller, class: RequestsAdmin
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,948 Enabling 'library' controller, class: Library
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,950 Enabling 'requests' controller, class: Requests
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,952 Enabling 'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,954 Enabling 'library_admin' controller, class: LibraryAdmin
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,955 Enabling 'tag' controller, class: TagsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,957 Enabling 'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2013-12-19 12:22:20,961 Enabling 'request_type' controller, class: RequestType
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,003 Enabling 'cloudlaunch' controller, class: CloudController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,004 Enabling 'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,004 Enabling 'external_services' controller, class: ExternalServiceController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,007 Enabling 'history' controller, class: HistoryController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,009 Enabling 'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,012 Enabling 'configuration' API controller, class: ConfigurationController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,013 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,014 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,015 Enabling 'samples' API controller, class: SamplesAPIController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,026 Enabling 'histories' API controller, class: HistoriesController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,027 Enabling 'folders' API controller, class: FoldersController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,029 Enabling 'request_types' API controller, class: RequestTypeAPIController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,030 Enabling 'datatypes' API controller, class: DatatypesController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,031 Enabling 'library_contents' API controller, class: LibraryContentsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,032 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,032 Enabling 'history_tags' API controller, class: HistoryTagsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,032 Enabling 'workflow_tags' API controller, class: WorkflowTagsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,042 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,042 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,042 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,043 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,074 Enabling 'search' API controller, class: SearchController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,075 Enabling 'history_contents' API controller, class: HistoryContentsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,075 Enabling 'genomes' API controller, class: GenomesController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,076 Enabling 'users' API controller, class: UserAPIController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,077 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,078 Enabling 'roles' API controller, class: RoleAPIController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,079 Enabling 'requests' API controller, class: RequestsAPIController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,081 Enabling 'group_users' API controller, class: GroupUsersAPIController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,081 Enabling 'groups' API controller, class: GroupAPIController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,090 Enabling 'visualizations' API controller, class: VisualizationsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,091 Enabling 'forms' API controller, class: FormDefinitionAPIController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,092 Enabling 'libraries' API controller, class: LibrariesController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,093 Enabling 'datasets' API controller, class: DatasetsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,094 Enabling 'permissions' API controller, class: PermissionsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,095 Enabling 'workflows' API controller, class: WorkflowsAPIController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,097 Enabling 'folder_contents' API controller, class: FolderContentsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,098 Enabling 'quotas' API controller, class: QuotaAPIController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,099 Enabling 'tools' API controller, class: ToolsController
galaxy.web.framework.base DEBUG 2013-12-19 12:22:21,100 Enabling 'group_roles' API controller, class: GroupRolesAPIController
galaxy.webapps.galaxy.buildapp DEBUG 2013-12-19 12:22:21,100 app.config.api_folders: False
galaxy.webapps.galaxy.buildapp DEBUG 2013-12-19 12:22:21,774 Enabling 'httpexceptions' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2013-12-19 12:22:21,776 Enabling 'recursive' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2013-12-19 12:22:21,781 Enabling 'error' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2013-12-19 12:22:21,781 Enabling 'x-forwarded-host' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2013-12-19 12:22:21,782 Enabling 'Request ID' middleware
functional_tests.py DEBUG 2013-12-19 12:22:21,789 Attempting to serve app on randomly chosen port: 8679
functional_tests.py INFO 2013-12-19 12:22:24,181 Embedded web server started
base.asserts DEBUG 2013-12-19 12:22:24,329 base.asserts.text
base.asserts DEBUG 2013-12-19 12:22:24,333 base.asserts.tabular
base.asserts DEBUG 2013-12-19 12:22:24,336 base.asserts.xml
functional_tests.py INFO 2013-12-19 12:22:24,347 Functional tests will be run against localhost:8679
nose.plugins.manager DEBUG 2013-12-19 12:22:24,370 DefaultPluginManager load plugin nosetestdiff = nosetestdiff.plugin:NoseTestDiff
nose.plugins.manager DEBUG 2013-12-19 12:22:24,372 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML

----------------------------------------------------------------------
Ran 0 tests in 0.001s

OK
functional_tests.py INFO 2013-12-19 12:22:24,507 Shutting down
functional_tests.py INFO 2013-12-19 12:22:24,507 Shutting down embedded web server
functional_tests.py INFO 2013-12-19 12:22:24,511 Embedded web server stopped
functional_tests.py INFO 2013-12-19 12:22:24,511 Shutting down app
galaxy.jobs.handler INFO 2013-12-19 12:22:24,512 sending stop signal to worker thread
galaxy.jobs.handler INFO 2013-12-19 12:22:24,512 job handler queue stopped
galaxy.jobs.runners INFO 2013-12-19 12:22:24,512 LWRRunner: Sending stop signal to monitor thread
galaxy.jobs.runners INFO 2013-12-19 12:22:24,513 LWRRunner: Sending stop signal to 3 worker threads
galaxy.jobs.runners INFO 2013-12-19 12:22:24,513 LocalRunner: Sending stop signal to 5 worker threads
galaxy.jobs.handler INFO 2013-12-19 12:22:24,514 sending stop signal to worker thread
galaxy.jobs.handler INFO 2013-12-19 12:22:24,515 job handler stop queue stopped
functional_tests.py INFO 2013-12-19 12:22:24,516 Embedded Universe application stopped
functional_tests.py INFO 2013-12-19 12:22:24,517 Cleaning up temporary files in /tmp/tmpAntFXD/tmpxBWOfe
galaxy.jobs.handler INFO 2013-12-19 12:22:25,114 sending stop signal to worker thread
galaxy.jobs.handler INFO 2013-12-19 12:22:25,114 job handler queue stopped
galaxy.jobs.runners INFO 2013-12-19 12:22:25,115 LWRRunner: Sending stop signal to monitor thread
galaxy.jobs.runners INFO 2013-12-19 12:22:25,115 LWRRunner: Sending stop signal to 3 worker threads
galaxy.jobs.runners INFO 2013-12-19 12:22:25,115 LocalRunner: Sending stop signal to 5 worker threads
galaxy.jobs.handler INFO 2013-12-19 12:22:25,116 sending stop signal to worker thread
galaxy.jobs.handler INFO 2013-12-19 12:22:25,116 job handler stop queue stopped
Exception OSError: (2, 'No such file or directory', '/tmp/tmpAntFXD/tmpxBWOfe/new_files_path_ElYcSt/tmphevm6e') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', mode 'w' at 0x2659e270>> ignored
'run_functional_tests.sh help'                  for help