API tools faq
paste
Advertisement
Guest User

Untitled

a guest
Mar 23rd, 2015
279
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 47.80 KB | None | 0 0
raw download clone embed print report
  1. (galaxy_env)galaxy@bioinfo-wstation-01:~/galaxy$ ./run.sh
  2. /mnt/work/galaxy/galaxy/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
  3. from csamtools import *
  4. python path is: /mnt/work/galaxy/galaxy/eggs/Babel-1.3-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/pytz-2013.9-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/mercurial-3.2.4-py2.6-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/PyYAML-3.10-py2.6-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/Mako-0.4.1-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/kombu-3.0.13-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/ordereddict-1.1-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/importlib-1.0.3-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/anyjson-0.3.3-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/WebHelpers-1.3-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/bx_python-0.7.2-py2.6-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/SQLAlchemy-0.9.8-py2.6-linux-x86_64-ucs4.egg, /mnt/work/galaxy/galaxy/eggs/WebOb-0.8.5-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/Routes-2.1-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/repoze.lru-0.6-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/amqp-1.4.5-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/pexpect-2.4-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/wchartype-0.1-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/docutils-0.7-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/PasteDeploy-1.5.0-py2.6.egg, /mnt/work/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.6.egg, /mnt/work/galaxy/galaxy/lib, /mnt/work/galaxy/galaxy/galaxy_env/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg, /mnt/work/galaxy/galaxy/galaxy_env/lib/python2.6/site-packages/pip-6.0.8-py2.6.egg, /mnt/work/galaxy/galaxy/galaxy_env/lib/python2.6/site-packages/elementtree-1.2.7_20070827_preview-py2.6.egg, /mnt/work/galaxy/galaxy/galaxy_env/lib/python2.6, /mnt/work/galaxy/galaxy/galaxy_env/lib/python2.6/plat-linux2, /mnt/work/galaxy/galaxy/galaxy_env/lib/python2.6/lib-tk, /mnt/work/galaxy/galaxy/galaxy_env/lib/python2.6/lib-old, /mnt/work/galaxy/galaxy/galaxy_env/lib/python2.6/lib-dynload, /usr/lib/python2.6, /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /mnt/work/galaxy/galaxy/galaxy_env/lib/python2.6/site-packages
  5. tool_shed.util.xml_util ERROR 2015-03-23 02:18:15,811 Exception attempting to parse ./config/tool_sheds_conf.xml.sample: No module named expat; use SimpleXMLTreeBuilder instead
  6. Traceback (most recent call last):
  7. File "/mnt/work/galaxy/galaxy/lib/tool_shed/util/xml_util.py", line 128, in parse_xml
  8. tree = XmlET.parse( fobj, parser=Py26CommentedTreeBuilder() )
  9. File "/mnt/work/galaxy/galaxy/lib/tool_shed/util/xml_util.py", line 17, in __init__
  10. XmlET.XMLTreeBuilder.__init__( self, html, target )
  11. File "/usr/lib/python2.6/xml/etree/ElementTree.py", line 1118, in __init__
  12. "No module named expat; use SimpleXMLTreeBuilder instead"
  13. ImportError: No module named expat; use SimpleXMLTreeBuilder instead
  14. tool_shed.tool_shed_registry WARNING 2015-03-23 02:18:15,811 Unable to load references to tool sheds defined in file ./config/tool_sheds_conf.xml.sample
  15. galaxy.app DEBUG 2015-03-23 02:18:15,811 Using "galaxy.ini" config file: /mnt/work/galaxy/galaxy/config/galaxy.ini.sample
  16. galaxy.eggs WARNING 2015-03-23 02:18:16,025 Warning: pbr (a dependent egg of sqlalchemy-migrate) cannot be fetched
  17. migrate.versioning.repository DEBUG 2015-03-23 02:18:16,082 Loading repository lib/galaxy/model/migrate...
  18. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,083 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
  19. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,083 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully
  20. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,083 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py...
  21. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,083 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully
  22. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,083 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py...
  23. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,083 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully
  24. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,083 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py...
  25. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,083 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully
  26. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,083 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py...
  27. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,083 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully
  28. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py...
  29. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully
  30. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py...
  31. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully
  32. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py...
  33. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully
  34. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py...
  35. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully
  36. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py...
  37. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully
  38. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py...
  39. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully
  40. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py...
  41. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully
  42. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py...
  43. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,084 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully
  44. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Loading script lib/galaxy/model/migrate/versions/0014_pages.py...
  45. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully
  46. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py...
  47. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully
  48. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py...
  49. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully
  50. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py...
  51. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully
  52. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py...
  53. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully
  54. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py...
  55. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully
  56. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py...
  57. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,085 Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded successfully
  58. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py...
  59. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Script lib/galaxy/model/migrate/versions/0021_user_prefs.py loaded successfully
  60. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py...
  61. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Script lib/galaxy/model/migrate/versions/0022_visualization_tables.py loaded successfully
  62. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py...
  63. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py loaded successfully
  64. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Loading script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py...
  65. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Script lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py loaded successfully
  66. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Loading script lib/galaxy/model/migrate/versions/0025_user_info.py...
  67. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Script lib/galaxy/model/migrate/versions/0025_user_info.py loaded successfully
  68. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Loading script lib/galaxy/model/migrate/versions/0026_cloud_tables.py...
  69. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Script lib/galaxy/model/migrate/versions/0026_cloud_tables.py loaded successfully
  70. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Loading script lib/galaxy/model/migrate/versions/0027_request_events.py...
  71. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Script lib/galaxy/model/migrate/versions/0027_request_events.py loaded successfully
  72. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Loading script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py...
  73. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,086 Script lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py loaded successfully
  74. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Loading script lib/galaxy/model/migrate/versions/0029_user_actions.py...
  75. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Script lib/galaxy/model/migrate/versions/0029_user_actions.py loaded successfully
  76. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Loading script lib/galaxy/model/migrate/versions/0030_history_slug_column.py...
  77. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Script lib/galaxy/model/migrate/versions/0030_history_slug_column.py loaded successfully
  78. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Loading script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py...
  79. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Script lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py loaded successfully
  80. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Loading script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py...
  81. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Script lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py loaded successfully
  82. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Loading script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py...
  83. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Script lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py loaded successfully
  84. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Loading script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py...
  85. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Script lib/galaxy/model/migrate/versions/0034_page_user_share_association.py loaded successfully
  86. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Loading script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py...
  87. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Script lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py loaded successfully
  88. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,087 Loading script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py...
  89. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Script lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py loaded successfully
  90. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Loading script lib/galaxy/model/migrate/versions/0037_samples_library.py...
  91. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Script lib/galaxy/model/migrate/versions/0037_samples_library.py loaded successfully
  92. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Loading script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py...
  93. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Script lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py loaded successfully
  94. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Loading script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py...
  95. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Script lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py loaded successfully
  96. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Loading script lib/galaxy/model/migrate/versions/0040_page_annotations.py...
  97. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Script lib/galaxy/model/migrate/versions/0040_page_annotations.py loaded successfully
  98. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Loading script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py...
  99. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Script lib/galaxy/model/migrate/versions/0041_workflow_invocation.py loaded successfully
  100. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Loading script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py...
  101. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Script lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py loaded successfully
  102. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Loading script lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py...
  103. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Script lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py loaded successfully
  104. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,088 Loading script lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py...
  105. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Script lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py loaded successfully
  106. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Loading script lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py...
  107. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Script lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py loaded successfully
  108. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Loading script lib/galaxy/model/migrate/versions/0046_post_job_actions.py...
  109. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Script lib/galaxy/model/migrate/versions/0046_post_job_actions.py loaded successfully
  110. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Loading script lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py...
  111. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Script lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py loaded successfully
  112. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Loading script lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py...
  113. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Script lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py loaded successfully
  114. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Loading script lib/galaxy/model/migrate/versions/0049_api_keys_table.py...
  115. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Script lib/galaxy/model/migrate/versions/0049_api_keys_table.py loaded successfully
  116. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Loading script lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py...
  117. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Script lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py loaded successfully
  118. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Loading script lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py...
  119. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Script lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py loaded successfully
  120. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,089 Loading script lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py...
  121. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Script lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py loaded successfully
  122. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Loading script lib/galaxy/model/migrate/versions/0053_item_ratings.py...
  123. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Script lib/galaxy/model/migrate/versions/0053_item_ratings.py loaded successfully
  124. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Loading script lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py...
  125. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Script lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py loaded successfully
  126. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Loading script lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py...
  127. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Script lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py loaded successfully
  128. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Loading script lib/galaxy/model/migrate/versions/0056_workflow_outputs.py...
  129. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Script lib/galaxy/model/migrate/versions/0056_workflow_outputs.py loaded successfully
  130. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Loading script lib/galaxy/model/migrate/versions/0057_request_notify.py...
  131. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Script lib/galaxy/model/migrate/versions/0057_request_notify.py loaded successfully
  132. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Loading script lib/galaxy/model/migrate/versions/0058_history_import_export.py...
  133. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Script lib/galaxy/model/migrate/versions/0058_history_import_export.py loaded successfully
  134. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Loading script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py...
  135. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,090 Script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py loaded successfully
  136. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Loading script lib/galaxy/model/migrate/versions/0060_history_archive_import.py...
  137. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Script lib/galaxy/model/migrate/versions/0060_history_archive_import.py loaded successfully
  138. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Loading script lib/galaxy/model/migrate/versions/0061_tasks.py...
  139. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Script lib/galaxy/model/migrate/versions/0061_tasks.py loaded successfully
  140. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Loading script lib/galaxy/model/migrate/versions/0062_user_openid_table.py...
  141. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Script lib/galaxy/model/migrate/versions/0062_user_openid_table.py loaded successfully
  142. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Loading script lib/galaxy/model/migrate/versions/0063_sequencer_table.py...
  143. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Script lib/galaxy/model/migrate/versions/0063_sequencer_table.py loaded successfully
  144. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Loading script lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py...
  145. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Script lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py loaded successfully
  146. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Loading script lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py...
  147. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Script lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py loaded successfully
  148. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Loading script lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py...
  149. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Script lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py loaded successfully
  150. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Loading script lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py...
  151. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,091 Script lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py loaded successfully
  152. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Loading script lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py...
  153. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Script lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py loaded successfully
  154. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Loading script lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py...
  155. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Script lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py loaded successfully
  156. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Loading script lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py...
  157. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Script lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py loaded successfully
  158. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Loading script lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py...
  159. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Script lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py loaded successfully
  160. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Loading script lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py...
  161. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Script lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py loaded successfully
  162. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Loading script lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py...
  163. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Script lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py loaded successfully
  164. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Loading script lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py...
  165. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Script lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py loaded successfully
  166. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Loading script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py...
  167. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,092 Script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py loaded successfully
  168. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Loading script lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py...
  169. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Script lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py loaded successfully
  170. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Loading script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py...
  171. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py loaded successfully
  172. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Loading script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py...
  173. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py loaded successfully
  174. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Loading script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py...
  175. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py loaded successfully
  176. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Loading script lib/galaxy/model/migrate/versions/0080_quota_tables.py...
  177. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Script lib/galaxy/model/migrate/versions/0080_quota_tables.py loaded successfully
  178. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Loading script lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py...
  179. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Script lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py loaded successfully
  180. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Loading script lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py...
  181. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Script lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py loaded successfully
  182. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,093 Loading script lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py...
  183. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Script lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py loaded successfully
  184. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Loading script lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py...
  185. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Script lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py loaded successfully
  186. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Loading script lib/galaxy/model/migrate/versions/0085_add_task_info.py...
  187. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Script lib/galaxy/model/migrate/versions/0085_add_task_info.py loaded successfully
  188. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Loading script lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py...
  189. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Script lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py loaded successfully
  190. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Loading script lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py...
  191. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Script lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py loaded successfully
  192. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Loading script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py...
  193. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py loaded successfully
  194. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Loading script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py...
  195. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py loaded successfully
  196. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Loading script lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py...
  197. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Script lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py loaded successfully
  198. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,094 Loading script lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py...
  199. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Script lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py loaded successfully
  200. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Loading script lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py...
  201. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Script lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py loaded successfully
  202. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Loading script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py...
  203. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py loaded successfully
  204. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Loading script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py...
  205. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py loaded successfully
  206. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Loading script lib/galaxy/model/migrate/versions/0095_hda_subsets.py...
  207. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Script lib/galaxy/model/migrate/versions/0095_hda_subsets.py loaded successfully
  208. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Loading script lib/galaxy/model/migrate/versions/0096_openid_provider.py...
  209. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Script lib/galaxy/model/migrate/versions/0096_openid_provider.py loaded successfully
  210. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Loading script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py...
  211. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py loaded successfully
  212. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Loading script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py...
  213. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,095 Script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py loaded successfully
  214. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Loading script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py...
  215. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py loaded successfully
  216. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Loading script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py...
  217. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py loaded successfully
  218. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Loading script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py...
  219. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully
  220. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Loading script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py...
  221. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully
  222. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py...
  223. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully
  224. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py...
  225. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully
  226. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py...
  227. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully
  228. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py...
  229. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,096 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully
  230. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py...
  231. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully
  232. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py...
  233. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully
  234. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py...
  235. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully
  236. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py...
  237. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py loaded successfully
  238. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Loading script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py...
  239. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py loaded successfully
  240. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Loading script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py...
  241. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py loaded successfully
  242. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Loading script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py...
  243. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded successfully
  244. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Loading script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py...
  245. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,097 Script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py loaded successfully
  246. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py...
  247. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully
  248. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Loading script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py...
  249. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully
  250. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py...
  251. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully
  252. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py...
  253. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully
  254. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py...
  255. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully
  256. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py...
  257. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully
  258. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py...
  259. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully
  260. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,098 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py...
  261. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully
  262. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py...
  263. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully
  264. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py...
  265. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully
  266. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py...
  267. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully
  268. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py...
  269. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully
  270. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py...
  271. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully
  272. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py...
  273. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,099 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully
  274. migrate.versioning.repository DEBUG 2015-03-23 02:18:16,099 Repository lib/galaxy/model/migrate loaded successfully
  275. migrate.versioning.repository DEBUG 2015-03-23 02:18:16,099 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}}
  276. galaxy.model.migrate.check DEBUG 2015-03-23 02:18:16,102 pysqlite>=2 egg successfully loaded for sqlite dialect
  277. galaxy.model.migrate.check INFO 2015-03-23 02:18:16,149 At database version 128
  278. migrate.versioning.repository DEBUG 2015-03-23 02:18:16,161 Loading repository lib/tool_shed/galaxy_install/migrate...
  279. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,161 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py...
  280. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,161 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully
  281. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,161 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py...
  282. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully
  283. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py...
  284. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully
  285. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py...
  286. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py loaded successfully
  287. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Loading script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py...
  288. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py loaded successfully
  289. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Loading script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py...
  290. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py loaded successfully
  291. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Loading script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py...
  292. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully
  293. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py...
  294. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully
  295. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py...
  296. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully
  297. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,162 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py...
  298. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,163 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully
  299. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,163 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py...
  300. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,163 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully
  301. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,163 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py...
  302. migrate.versioning.script.base DEBUG 2015-03-23 02:18:16,163 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully
  303. migrate.versioning.repository DEBUG 2015-03-23 02:18:16,163 Repository lib/tool_shed/galaxy_install/migrate loaded successfully
  304. migrate.versioning.repository DEBUG 2015-03-23 02:18:16,163 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_tools', 'repository_id': 'GalaxyTools'}}
  305. tool_shed.galaxy_install.migrate.check DEBUG 2015-03-23 02:18:16,165 pysqlite>=2 egg successfully loaded for sqlite dialect
  306. tool_shed.galaxy_install.migrate.check INFO 2015-03-23 02:18:16,180 At migrate_tools version 12
  307. galaxy.model.orm DEBUG 2015-03-23 02:18:16,182 pysqlite>=2 egg successfully loaded for sqlite dialect
  308. galaxy.config INFO 2015-03-23 02:18:16,268 Install database targetting Galaxy's database configuration.
  309. Traceback (most recent call last):
  310. File "/mnt/work/galaxy/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 53, in app_factory
  311. app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
  312. File "/mnt/work/galaxy/galaxy/lib/galaxy/app.py", line 55, in __init__
  313. self._configure_datatypes_registry( self.installed_repository_manager )
  314. File "/mnt/work/galaxy/galaxy/lib/galaxy/config.py", line 782, in _configure_datatypes_registry
  315. self.datatypes_registry.load_datatypes( self.config.root, datatypes_config, override=True )
  316. File "/mnt/work/galaxy/galaxy/lib/galaxy/datatypes/registry.py", line 102, in load_datatypes
  317. tree = galaxy.util.parse_xml( config )
  318. File "/mnt/work/galaxy/galaxy/lib/galaxy/util/__init__.py", line 177, in parse_xml
  319. root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) )
  320. File "/usr/lib/python2.6/xml/etree/ElementTree.py", line 1118, in __init__
  321. "No module named expat; use SimpleXMLTreeBuilder instead"
  322. ImportError: No module named expat; use SimpleXMLTreeBuilder instead
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement
Public Pastes
Advertisement
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!