API tools faq
paste
Advertisement
Guest User

run_functional_tests_srma_wrapper

a guest
Jun 16th, 2011
105
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
Bash 95.88 KB | None | 0 0
raw download clone embed print report
  1. udp035588uds:sr_mapping user$ cd ~/galaxy-dist/
  2. udp035588uds:galaxy-dist user$ sh run_functional_tests.sh - id srma_wrapper
  3. Database connection: sqlite:////var/folders/gq/gquONqXXGUGk1+4cFi9O8U+++TM/-Tmp-/tmpEQ3_W-/database/universe.sqlite
  4. python path is: /Users/user/galaxy-dist/eggs/numpy-1.3.0-py2.4-macosx-10.3-fat-ucs2.egg, /Users/user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.4-macosx-10.3-fat-ucs2.egg, /Users/user/galaxy-dist/eggs/ctypes-1.0.2-py2.4-macosx-10.3-fat-ucs2.egg, /Users/user/galaxy-dist/eggs/Whoosh-0.3.18-py2.4.egg, /Users/user/galaxy-dist/eggs/pycrypto-2.0.1-py2.4-macosx-10.3-fat-ucs2.egg, /Users/user/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.4-macosx-10.3-fat-ucs2.egg, /Users/user/galaxy-dist/eggs/bx_python-0.7.0_494c2d1d68b3-py2.4-macosx-10.3-fat-ucs2.egg, /Users/user/galaxy-dist/eggs/amqplib-0.6.1-py2.4.egg, /Users/user/galaxy-dist/eggs/pexpect-2.4-py2.4.egg, /Users/user/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg, /Users/user/galaxy-dist/eggs/Babel-0.9.4-py2.4.egg, /Users/user/galaxy-dist/eggs/Beaker-1.4-py2.4.egg, /Users/user/galaxy-dist/eggs/Mako-0.2.5-py2.4.egg, /Users/user/galaxy-dist/eggs/WebHelpers-0.2-py2.4.egg, /Users/user/galaxy-dist/eggs/simplejson-2.1.1-py2.4-macosx-10.3-fat-ucs2.egg, /Users/user/galaxy-dist/eggs/WebOb-0.8.5-py2.4.egg, /Users/user/galaxy-dist/eggs/Routes-1.12.3-py2.4.egg, /Users/user/galaxy-dist/eggs/wchartype-0.1-py2.4.egg, /Users/user/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.4.egg, /Users/user/galaxy-dist/eggs/docutils-0.7-py2.4.egg, /Users/user/galaxy-dist/eggs/twill-0.9-py2.4.egg/twill/other_packages, /Users/user/galaxy-dist/eggs/pysqlite-2.5.6_3.6.17_static-py2.4-macosx-10.3-fat-ucs2.egg, /Users/user/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-macosx-10.3-fat-ucs2.egg, /Users/user/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg, /Users/user/galaxy-dist/eggs/Paste-1.6-py2.4.egg, /Users/user/galaxy-dist/eggs/twill-0.9-py2.4.egg, /Users/user/galaxy-dist/eggs/NoseTestDiff-0.1-py2.4.egg, /Users/user/galaxy-dist/eggs/NoseHTML-0.4.1-py2.4.egg, /Users/user/galaxy-dist/eggs/nose-0.11.1-py2.4.egg, /Users/user/galaxy-dist/lib, /Library/Frameworks/Python.framework/Versions/2.4/lib/python24.zip, /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4, /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/plat-darwin, /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/plat-mac, /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/plat-mac/lib-scriptpackages, /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/lib-tk, /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/lib-dynload, /Library/Frameworks/Python.framework/Versions/2.4/lib/python2.4/site-packages, /Users/user/galaxy-dist/eggs/twill-0.9-py2.4.egg/twill/extensions
  5. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,081 Loading datatypes from datatypes_conf.xml
  6. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,158 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False
  7. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,179 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False
  8. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,180 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False
  9. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,184 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False
  10. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,187 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False
  11. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,201 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True
  12. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,202 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True
  13. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,209 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True
  14. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,212 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True
  15. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,216 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False
  16. galaxy.datatypes.assembly DEBUG 2011-06-16 11:20:38,217 Velvet log info  JJ __init__
  17. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,227 Loaded sniffer for datatype: galaxy.datatypes.binary:Bam
  18. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,227 Loaded sniffer for datatype: galaxy.datatypes.binary:Sff
  19. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,227 Loaded sniffer for datatype: galaxy.datatypes.xml:BlastXml
  20. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,227 Loaded sniffer for datatype: galaxy.datatypes.sequence:Maf
  21. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,227 Loaded sniffer for datatype: galaxy.datatypes.sequence:Lav
  22. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,227 Loaded sniffer for datatype: galaxy.datatypes.sequence:csFasta
  23. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,227 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScoreSOLiD
  24. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,228 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScore454
  25. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,228 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fasta
  26. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,228 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fastq
  27. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,228 Loaded sniffer for datatype: galaxy.datatypes.interval:Wiggle
  28. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,228 Loaded sniffer for datatype: galaxy.datatypes.images:Html
  29. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,228 Loaded sniffer for datatype: galaxy.datatypes.images:Pdf
  30. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,228 Loaded sniffer for datatype: galaxy.datatypes.sequence:Axt
  31. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,229 Loaded sniffer for datatype: galaxy.datatypes.interval:Bed
  32. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,229 Loaded sniffer for datatype: galaxy.datatypes.interval:CustomTrack
  33. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,229 Loaded sniffer for datatype: galaxy.datatypes.interval:Gtf
  34. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,229 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff
  35. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,229 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff3
  36. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,229 Loaded sniffer for datatype: galaxy.datatypes.tabular:Pileup
  37. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,230 Loaded sniffer for datatype: galaxy.datatypes.interval:Interval
  38. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,230 Loaded sniffer for datatype: galaxy.datatypes.tabular:Sam
  39. galaxy.datatypes.registry DEBUG 2011-06-16 11:20:38,230 Loaded sniffer for datatype: galaxy.datatypes.tabular:Vcf
  40. galaxy.model.migrate.check DEBUG 2011-06-16 11:20:38,453 pysqlite>=2 egg successfully loaded for sqlite dialect
  41. galaxy.model.migrate.check INFO 2011-06-16 11:20:38,530 No database, initializing
  42. galaxy.model.migrate.check INFO 2011-06-16 11:20:38,557 Migrating 0 -> 1...
  43. galaxy.model.migrate.check INFO 2011-06-16 11:20:39,114
  44. galaxy.model.migrate.check INFO 2011-06-16 11:20:39,114 Migrating 1 -> 2...
  45. galaxy.model.migrate.check INFO 2011-06-16 11:20:39,178
  46. galaxy.model.migrate.check INFO 2011-06-16 11:20:39,178 Migrating 2 -> 3...
  47. galaxy.model.custom_types DEBUG 2011-06-16 11:20:40,196 Adding foreign key constraint 'history_dataset_association_copied_from_library_dataset_da_fkey' to table 'history_dataset_association' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "history_dataset_association" ADD CONSTRAINT history_dataset_association_copied_from_library_dataset_da_fkey FOREIGN KEY (copied_from_library_dataset_dataset_association_id) REFERENCES library_dataset_dataset_association (id)' ()
  48. galaxy.model.custom_types DEBUG 2011-06-16 11:20:40,196 Adding foreign key constraint 'metadata_file_lda_id_fkey' to table 'metadata_file' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "metadata_file" ADD CONSTRAINT metadata_file_lda_id_fkey FOREIGN KEY (lda_id) REFERENCES library_dataset_dataset_association (id)' ()
  49. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,199
  50. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,199 Migrating 3 -> 4...
  51. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,298
  52. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,298 Migrating 4 -> 5...
  53. galaxy.model.custom_types DEBUG 2011-06-16 11:20:40,343 Fixing a discrepancy concerning deleted shared history items.
  54. galaxy.model.custom_types DEBUG 2011-06-16 11:20:40,645 0 items affected, and restored.
  55. galaxy.model.custom_types DEBUG 2011-06-16 11:20:40,646 Time elapsed: 0.302360057831
  56. galaxy.model.custom_types DEBUG 2011-06-16 11:20:40,646 Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs.
  57. galaxy.model.custom_types DEBUG 2011-06-16 11:20:40,647 0 items affected, and restored.
  58. galaxy.model.custom_types DEBUG 2011-06-16 11:20:40,647 Time elapsed: 0.00132203102112
  59. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,650
  60. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,650 Migrating 5 -> 6...
  61. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,746 ========================================
  62. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,747 This migration script changes certain values in the history_dataset_association.extension
  63. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,747 column, specifically 'qual' is chaged to be 'qual454'.
  64. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,747 ========================================
  65. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,747
  66. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,747 Migrating 6 -> 7...
  67. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,841 ========================================
  68. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,842 This migration script creates the new history_user_share_association table, and adds
  69. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,842 a new boolean type column to the history table.  This provides support for sharing
  70. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,842 histories in the same way that workflows are shared.
  71. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,842 ========================================
  72. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,842
  73. galaxy.model.migrate.check INFO 2011-06-16 11:20:40,842 Migrating 7 -> 8...
  74. galaxy.model.custom_types DEBUG 2011-06-16 11:20:40,982 Adding foreign key constraint 'form_definition_current_latest_form_id_fk' to table 'form_definition_current' failed: (OperationalError) near "CONSTRAINT": syntax error '\nALTER TABLE "form_definition_current" ADD CONSTRAINT form_definition_current_latest_form_id_fk FOREIGN KEY (latest_form_id) REFERENCES form_definition (id)' ()
  75. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,033 ========================================
  76. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 This migration script adds the following new tables for supporting Galaxy forms:
  77. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 1) form_definition_current
  78. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 2) form_definition
  79. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 3) form_values
  80. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 4) request_type
  81. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 5) request
  82. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 6) sample
  83. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 7) sample_state
  84. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 8) sample_event
  85. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 ========================================
  86. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034
  87. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,034 Migrating 8 -> 9...
  88. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,160 ========================================
  89. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,160 This migration script adds a new column to 2 tables:
  90. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,160 1) a new boolean type column named 'submitted' to the 'request' table
  91. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,160 2) a new string type column named 'bar_code' to the 'sample' table
  92. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,160 ========================================
  93. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,161
  94. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,161 Migrating 9 -> 10...
  95. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,270 ========================================
  96. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,270 This migration script adds the history_dataset_association_display_at_authorization table, which
  97. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,271 allows 'private' datasets to be displayed at external sites without making them public.
  98. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,271
  99. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,271 If using mysql, this script will display the following error, which is corrected in the next migration
  100. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,271 script: history_dataset_association_display_at_authorization table failed:  (OperationalError)
  101. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,271 (1059, 'Identifier name  'ix_history_dataset_association_display_at_authorization_update_time'
  102. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,271 is too long.
  103. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,271 ========================================
  104. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,271
  105. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,271 Migrating 10 -> 11...
  106. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,280 ========================================
  107. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,280 This script fixes a problem introduced in the previous migration script ( 9->10 ).  MySQL
  108. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,280 has a name length limit and thus the index 'ix_hdadaa_history_dataset_association_id' has
  109. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,280 to be manually created.
  110. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,280 ========================================
  111. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,280
  112. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,280 Migrating 11 -> 12...
  113. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,444 ========================================
  114. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,444 This script adds a new user_address table that is currently only used with sample requests, where
  115. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,444 a user can select from a list of his addresses to associate with the request.  This script also
  116. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,444 drops the request.submitted column which was boolean and replaces it with a request.state column
  117. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,445 which is a string, allowing for more flexibility with request states.
  118. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,445 ========================================
  119. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,445
  120. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,445 Migrating 12 -> 13...
  121. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691 ========================================
  122. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691 This migration script eliminates all of the tables that were used for the 1st version of the
  123. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691 library templates where template fields and contents were each stored as a separate table row
  124. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691 in various library item tables.  All of these tables are dropped in this script, eliminating all
  125. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691 existing template data.  A total of 14 existing tables are dropped.
  126. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691
  127. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691 We're now basing library templates on Galaxy forms, so field contents are stored as a jsonified
  128. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691 list in the form_values table.  This script introduces the following 3 new association tables:
  129. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691 1) library_info_association
  130. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691 2) library_folder_info_association
  131. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691 3) library_dataset_dataset_info_association
  132. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,691
  133. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,692 If using mysql, this script will throw an (OperationalError) exception due to a long index name
  134. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,692 on the library_dataset_dataset_info_association table, which is OK because the script creates
  135. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,692 an index with a shortened name.
  136. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,692 ========================================
  137. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,692
  138. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,692 Migrating 13 -> 14...
  139. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,803
  140. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,803 Migration script to add support for "Pages".
  141. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,803   1) Creates Page and PageRevision tables
  142. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,803   2) Adds username column to User table
  143. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,803
  144. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,803
  145. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,803 Migrating 14 -> 15...
  146. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,991
  147. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,991 This migration script adds the tables necessary to support tagging of histories,
  148. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,991 datasets, and history-dataset associations (user views of datasets).
  149. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,991
  150. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,991 If using mysql, this script will display the following error, which is
  151. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,991 corrected in the next migration script:
  152. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,992 history_dataset_association_tag_association table failed:  
  153. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,992 (OperationalError) (1059, 'Identifier name
  154. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,992 'ix_history_dataset_association_tag_association_history_dataset_association_id'
  155. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,992 is too long)
  156. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,992
  157. galaxy.model.migrate.check INFO 2011-06-16 11:20:41,992 Migrating 15 -> 16...
  158. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,152
  159. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,152 This script fixes a problem introduced in 0015_tagging.py.  MySQL has a
  160. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,152 name length limit and thus the index 'ix_hda_ta_history_dataset_association_id'
  161. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,152 has to be manually created.
  162. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,152
  163. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,152 Migrating 16 -> 17...
  164. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,278 ========================================
  165. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,278 This script adds 3 indexes to table columns: library_folder.name,
  166. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,278 library_dataset.name, library_dataset_dataset_association.name.
  167. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,278 ========================================
  168. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,278
  169. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,279 Migrating 17 -> 18...
  170. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,530
  171. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,530 This migration script provides support for (a) ordering tags by recency and
  172. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,530 (b) tagging pages. This script deletes all existing tags.
  173. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,530
  174. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,530 Migrating 18 -> 19...
  175. 0019_request_library_folder DEBUG 2011-06-16 11:20:42,627 Adding foreign key constraint 'request_folder_id_fk' to table 'library_folder' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "request" ADD CONSTRAINT request_folder_id_fk FOREIGN KEY (folder_id) REFERENCES library_folder (id)' ()
  176. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,635 ========================================
  177. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,635 This script creates a request.folder_id column which is a foreign
  178. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,635 key to the library_folder table. This also adds a 'type' and 'layout' column
  179. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,636 to the form_definition table.
  180. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,636 ========================================
  181. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,636 0019_request_library_folder DEBUG 2011-06-16 11:20:42,627 Adding foreign key constraint 'request_folder_id_fk' to table 'library_folder' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "request" ADD CONSTRAINT request_folder_id_fk FOREIGN KEY (folder_id) REFERENCES library_folder (id)' ()
  182. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,636 0019_request_library_folder DEBUG 2011-06-16 11:20:42,627 Adding foreign key constraint 'request_folder_id_fk' to table 'library_folder' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "request" ADD CONSTRAINT request_folder_id_fk FOREIGN KEY (folder_id) REFERENCES library_folder (id)' ()
  183. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,636
  184. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,636 Migrating 19 -> 20...
  185. 0020_library_upload_job DEBUG 2011-06-16 11:20:42,763 Adding foreign key constraint 'job_library_folder_id_fk' to table 'library_folder' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "job" ADD CONSTRAINT job_library_folder_id_fk FOREIGN KEY (library_folder_id) REFERENCES library_folder (id)' ()
  186. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,769
  187. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,769 ========================================
  188. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,769 This script creates a job_to_output_library_dataset table for allowing library
  189. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,769 uploads to run as regular jobs.  To support this, a library_folder_id column is
  190. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,769 added to the job table, and library_folder/output_library_datasets relations
  191. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,769 are added to the Job object.  An index is also added to the dataset.state
  192. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,769 column.
  193. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,769 ========================================
  194. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,770 0020_library_upload_job DEBUG 2011-06-16 11:20:42,763 Adding foreign key constraint 'job_library_folder_id_fk' to table 'library_folder' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "job" ADD CONSTRAINT job_library_folder_id_fk FOREIGN KEY (library_folder_id) REFERENCES library_folder (id)' ()
  195. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,770 0020_library_upload_job DEBUG 2011-06-16 11:20:42,763 Adding foreign key constraint 'job_library_folder_id_fk' to table 'library_folder' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "job" ADD CONSTRAINT job_library_folder_id_fk FOREIGN KEY (library_folder_id) REFERENCES library_folder (id)' ()
  196. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,770
  197. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,770 Migrating 20 -> 21...
  198. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,875
  199. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,875 This migration script adds a user preferences table to Galaxy.
  200. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,875
  201. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,875
  202. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,875 Migrating 21 -> 22...
  203. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,988
  204. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,988 Migration script to add support for storing visualizations.
  205. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,988   1) Creates Visualization and VisualizationRevision tables
  206. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,988
  207. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,988
  208. galaxy.model.migrate.check INFO 2011-06-16 11:20:42,988 Migrating 22 -> 23...
  209. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,129
  210. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,130 Migration script to add columns for tracking whether pages are deleted and
  211. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,130 publicly accessible.
  212. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,130
  213. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,130
  214. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,130 Migrating 23 -> 24...
  215. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,235
  216. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,235 Remove unique constraint from page slugs to allow creating a page with
  217. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,235 the same slug as a deleted page.
  218. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,235
  219. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,235
  220. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,235 Migrating 24 -> 25...
  221. 0025_user_info DEBUG 2011-06-16 11:20:43,337 Adding foreign key constraint 'user_form_values_id_fk' to table 'galaxy_user' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "galaxy_user" ADD CONSTRAINT user_form_values_id_fk FOREIGN KEY (form_values_id) REFERENCES form_values (id)' ()
  222. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,340 ========================================
  223. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,340 This script adds a foreign key to the form_values table in the galaxy_user table
  224. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,340 ========================================
  225. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,340 0025_user_info DEBUG 2011-06-16 11:20:43,337 Adding foreign key constraint 'user_form_values_id_fk' to table 'galaxy_user' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "galaxy_user" ADD CONSTRAINT user_form_values_id_fk FOREIGN KEY (form_values_id) REFERENCES form_values (id)' ()
  226. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,340 0025_user_info DEBUG 2011-06-16 11:20:43,337 Adding foreign key constraint 'user_form_values_id_fk' to table 'galaxy_user' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "galaxy_user" ADD CONSTRAINT user_form_values_id_fk FOREIGN KEY (form_values_id) REFERENCES form_values (id)' ()
  227. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,340
  228. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,340 Migrating 25 -> 26...
  229. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,590
  230. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,590 ========================================
  231. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,590 This script adds tables needed for Galaxy cloud functionality.
  232. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,591 ========================================
  233. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,591
  234. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,591 Migrating 26 -> 27...
  235. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,731 ========================================
  236. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,731 This migration script adds the request_event table and
  237. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,731 removes the state field in the request table
  238. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,731 ========================================
  239. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,731
  240. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,731 Migrating 27 -> 28...
  241. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,853 ========================================
  242. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,853 This script adds the filename_override_metadata column to the JobExternalOutputMetadata table,
  243. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,853  allowing existing metadata files to be written when using external metadata and a cluster
  244. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,853 set up with read-only access to database/files
  245. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,853 ========================================
  246. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,853
  247. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,854 Migrating 28 -> 29...
  248. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,979
  249. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,980 This migration script adds a user actions table to Galaxy.
  250. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,980
  251. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,980
  252. galaxy.model.migrate.check INFO 2011-06-16 11:20:43,980 Migrating 29 -> 30...
  253. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,139
  254. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,140 Migration script to add column for a history slug.
  255. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,140
  256. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,140
  257. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,140 Migrating 30 -> 31...
  258. 0031_community_and_workflow_tags DEBUG 2011-06-16 11:20:44,267 Adding user_id column to history_tag_association table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  259. 0031_community_and_workflow_tags DEBUG 2011-06-16 11:20:44,275 Adding user_id column to history_dataset_association_tag_association table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  260. 0031_community_and_workflow_tags DEBUG 2011-06-16 11:20:44,284 Adding user_id column to history_tag_association table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  261. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,376
  262. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,376 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.
  263. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,377
  264. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,377 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.
  265. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,377
  266. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,377 SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  267. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,377 SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  268. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,377 SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  269. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,377
  270. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,377 Migrating 31 -> 32...
  271. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,509
  272. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,510 Migration script to add slug column for stored workflow.
  273. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,510
  274. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,510
  275. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,510 Migrating 32 -> 33...
  276. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,645
  277. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,646 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.
  278. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,646
  279. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,646
  280. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,646 Migrating 33 -> 34...
  281. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,786
  282. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,786 Migration script to create a table for page-user share association.
  283. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,786
  284. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,786
  285. galaxy.model.migrate.check INFO 2011-06-16 11:20:44,786 Migrating 34 -> 35...
  286. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,125
  287. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,125 Migration script to (a) create tables for annotating objects and (b) create tags for workflow steps.
  288. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,125
  289. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,125
  290. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,125 Migrating 35 -> 36...
  291. 0036_add_deleted_column_to_library_template_assoc_tables DEBUG 2011-06-16 11:20:45,256 deleted to false in library_info_association failed: global name 'db_session' is not defined
  292. 0036_add_deleted_column_to_library_template_assoc_tables DEBUG 2011-06-16 11:20:45,260 deleted to false in library_folder_info_association failed: global name 'db_session' is not defined
  293. 0036_add_deleted_column_to_library_template_assoc_tables DEBUG 2011-06-16 11:20:45,262 deleted to false in library_dataset_dataset_info_association failed: global name 'db_session' is not defined
  294. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,265
  295. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,265 Migration script to add a deleted column to the following tables:
  296. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,265 library_info_association, library_folder_info_association, library_dataset_dataset_info_association.
  297. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,265
  298. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,265
  299. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,266 Migrating 36 -> 37...
  300. 0037_samples_library DEBUG 2011-06-16 11:20:45,426 Adding column 'library_id' to sample table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  301. 0037_samples_library DEBUG 2011-06-16 11:20:45,429 Adding column 'folder_id' to sample table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  302. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,432
  303. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,432 This migration script removes the library_id & folder_id fields in the 'request' table and
  304. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,432 adds the same to the 'sample' table. This also adds a 'datatx' column to request_type table
  305. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,432 to store the sequencer login information. Finally, this adds a 'dataset_files' column to
  306. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,432 the sample table.
  307. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,433
  308. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,433 0037_samples_library DEBUG 2011-06-16 11:20:45,426 Adding column 'library_id' to sample table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  309. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,433 0037_samples_library DEBUG 2011-06-16 11:20:45,426 Adding column 'library_id' to sample table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  310. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,433 0037_samples_library DEBUG 2011-06-16 11:20:45,429 Adding column 'folder_id' to sample table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  311. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,433 0037_samples_library DEBUG 2011-06-16 11:20:45,429 Adding column 'folder_id' to sample table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  312. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,433
  313. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,433 Migrating 37 -> 38...
  314. 0038_add_inheritable_column_to_library_template_assoc_tables DEBUG 2011-06-16 11:20:45,565 Setting value of column inheritable to false in library_info_association failed: global name 'db_session' is not defined
  315. 0038_add_inheritable_column_to_library_template_assoc_tables DEBUG 2011-06-16 11:20:45,567 Setting value of column inheritable to false in library_folder_info_association failed: global name 'db_session' is not defined
  316. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,570
  317. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,570 Migration script to add an inheritable column to the following tables:
  318. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,570 library_info_association, library_folder_info_association.
  319. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,570 Also, in case of sqlite check if the previous migration script deleted the
  320. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,570 request table and if so, restore the table.
  321. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,570
  322. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,570
  323. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,570 Migrating 38 -> 39...
  324. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,704
  325. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,705 Migration script to add a synopsis column to the library table.
  326. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,705
  327. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,705
  328. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,705 Migrating 39 -> 40...
  329. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,846
  330. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,846 Migration script to (a) create tables for annotating pages.
  331. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,846
  332. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,846
  333. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,846 Migrating 40 -> 41...
  334. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,998
  335. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,999 Migration script to create tables for tracking workflow invocations.
  336. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,999
  337. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,999
  338. galaxy.model.migrate.check INFO 2011-06-16 11:20:45,999 Migrating 41 -> 42...
  339. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,295
  340. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,295 Drop and readd workflow invocation tables, allowing null jobs
  341. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,295
  342. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,295
  343. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,296 Migrating 42 -> 43...
  344. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,643
  345. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,643 Migration script to create tables and columns for sharing visualizations.
  346. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,643
  347. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,644
  348. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,644 Migrating 43 -> 44...
  349. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,782
  350. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,782 Migration script to add a notify column to the request table.
  351. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,782
  352. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,782
  353. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,782 Migrating 44 -> 45...
  354. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,943
  355. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,943 Migration script to add the request_type_permissions table.
  356. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,943
  357. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,943
  358. galaxy.model.migrate.check INFO 2011-06-16 11:20:46,944 Migrating 45 -> 46...
  359. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,095
  360. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,095 Migration script to create tables for handling post-job actions.
  361. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,095
  362. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,095
  363. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,095 Migrating 46 -> 47...
  364. 0047_job_table_user_id_column DEBUG 2011-06-16 11:20:47,237 Adding column 'user_id' to job table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  365. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,242
  366. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,242 Add a user_id column to the job table.
  367. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,242
  368. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,242 0047_job_table_user_id_column DEBUG 2011-06-16 11:20:47,237 Adding column 'user_id' to job table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  369. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,242 0047_job_table_user_id_column DEBUG 2011-06-16 11:20:47,237 Adding column 'user_id' to job table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  370. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,242 Updating user_id column in job table for  0  rows...
  371. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,242
  372. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,243 Updated the user_id column for  0  rows in the job table.  
  373. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,243 0  rows have no user_id since the value was NULL in the galaxy_session table.
  374. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,243
  375. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,243
  376. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,268 Migrating 47 -> 48...
  377. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,475
  378. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,475 Add a state column to the history_dataset_association and library_dataset_dataset_association table.
  379. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,476
  380. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,476
  381. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,476 Migrating 48 -> 49...
  382. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,627
  383. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,627 Migration script to add the api_keys table.
  384. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,627
  385. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,627
  386. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,627 Migrating 49 -> 50...
  387. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,972
  388. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,972 ========================================
  389. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,972 This script drops tables that were associated with the old Galaxy Cloud functionality.
  390. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,972 ========================================
  391. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,972
  392. galaxy.model.migrate.check INFO 2011-06-16 11:20:47,972 Migrating 50 -> 51...
  393. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,157
  394. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,157 Migration script to add imported column for jobs table.
  395. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,157
  396. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,157
  397. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,157 Migrating 51 -> 52...
  398. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,305
  399. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,305 Migration script to add the sample_dataset table and remove the 'dataset_files' column
  400. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,305 from the 'sample' table
  401. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,305
  402. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,305
  403. galaxy.model.migrate.check INFO 2011-06-16 11:20:48,305 Migrating 52 -> 53...
  404. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,178
  405. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,178 Migration script to create tables for rating histories, datasets, workflows, pages, and visualizations.
  406. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,178
  407. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,178
  408. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,178 Migrating 53 -> 54...
  409. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,376
  410. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,377 Migration script to add dbkey column for visualization.
  411. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,377
  412. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,377
  413. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,377 Migrating 54 -> 55...
  414. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,521
  415. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,521 Migration script to add the post_job_action_association table.
  416. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,521
  417. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,521
  418. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,521 Migrating 55 -> 56...
  419. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,705
  420. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,705 Migration script to create tables for adding explicit workflow outputs.
  421. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,705
  422. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,705
  423. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,705 Migrating 56 -> 57...
  424. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,862
  425. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,862 Migration script to modify the 'notify' field in the 'request' table from a boolean
  426. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,862 to a JSONType
  427. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,863
  428. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,863
  429. galaxy.model.migrate.check INFO 2011-06-16 11:20:49,863 Migrating 57 -> 58...
  430. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,198
  431. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,198 Migration script to create table for exporting histories to archives.
  432. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,198
  433. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,198
  434. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,198 Migrating 58 -> 59...
  435. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,353
  436. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,353 Migration script to modify the 'file_path' field type in 'sample_dataset' table
  437. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,353 to 'TEXT' so that it can support large file paths exceeding 255 characters
  438. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,353
  439. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,353
  440. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,353 Migrating 59 -> 60...
  441. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,512
  442. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,512 Migration script to create column and table for importing histories from
  443. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,512 file archives.
  444. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,512
  445. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,512
  446. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,512 Migrating 60 -> 61...
  447. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,679
  448. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,679 Migration script to create tables task management.
  449. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,679
  450. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,679
  451. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,679 Migrating 61 -> 62...
  452. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,836
  453. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,836 Migration script to create table for associating sessions and users with
  454. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,836 OpenIDs.
  455. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,836
  456. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,837
  457. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,837 Migrating 62 -> 63...
  458. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,996
  459. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,996 Migration script to create a new 'sequencer' table
  460. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,996
  461. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,997
  462. galaxy.model.migrate.check INFO 2011-06-16 11:20:50,997 Migrating 63 -> 64...
  463. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,176
  464. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,177 Migration script to add the run and sample_run_association tables.
  465. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,177
  466. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,177
  467. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,177 Migrating 64 -> 65...
  468. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,342
  469. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,342 Migration script to add 'name' attribute to the JSON dict which describes
  470. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,342 a form definition field and the form values in the database. In the 'form_values'
  471. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,342 table, the 'content' column is now a JSON dict instead of a list.
  472. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,343
  473. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,343
  474. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,343 Migrating 65 -> 66...
  475. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,712
  476. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,713 Migration script to create table for storing deferred job and managed transfer
  477. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,713 information.
  478. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,713
  479. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,713
  480. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,713 Migrating 66 -> 67...
  481. 0067_populate_sequencer_table DEBUG 2011-06-16 11:20:51,867 Creating column 'sequencer_id' in the 'request_type' table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  482. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,885
  483. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,885 Migration script to populate the 'sequencer' table and it is populated using unique
  484. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,885 entries in the 'datatx_info' column in the 'request_type' table. It also deletes the 'datatx_info'
  485. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,885 column in the 'request_type' table and adds a foreign key to the 'sequencer' table. The
  486. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,885 actual contents of the datatx_info column are stored as form_values.
  487. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,885
  488. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,885
  489. galaxy.model.migrate.check INFO 2011-06-16 11:20:51,885 Migrating 67 -> 68...
  490. 0068_rename_sequencer_to_external_services DEBUG 2011-06-16 11:20:52,048 Adding foreign key constraint 'sample_dataset_external_services_id_fk' to table 'sample_dataset' failed: (OperationalError) near "CONSTRAINT": syntax error u'\nALTER TABLE "sample_dataset" ADD CONSTRAINT sample_dataset_external_services_id_fk FOREIGN KEY (external_service_id) REFERENCES sequencer (id)' ()
  491. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,122
  492. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,122 This migration script renames the sequencer table to 'external_service' table and
  493. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,122 creates a association table, 'request_type_external_service_association' and
  494. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,122 populates it. The 'sequencer_id' foreign_key from the 'request_type' table is removed.
  495. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,122 The 'sequencer_type_id' column is renamed to 'external_service_type_id' in the renamed
  496. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,122 table 'external_service'. Finally, adds a foreign key to the external_service table in the
  497. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,123 sample_dataset table and populates it.
  498. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,123
  499. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,123
  500. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,123 Migrating 68 -> 69...
  501. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,280
  502. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,280 Migration script to rename the sequencer information form type to external service information form
  503. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,280
  504. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,280
  505. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,280 Migrating 69 -> 70...
  506. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,436
  507. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,436 Migration script to add 'info' column to the transfer_job table.
  508. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,436
  509. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,436
  510. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,436 Migrating 70 -> 71...
  511. 0071_add_history_and_workflow_to_sample DEBUG 2011-06-16 11:20:52,602 Adding history and workflow columns to sample table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  512. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,606
  513. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,606 Migration script to add 'workflow' and 'history' columns for a sample.
  514. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,606
  515. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,606 Adding history and workflow columns to sample table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  516. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,606
  517. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,606 Migrating 71 -> 72...
  518. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,768
  519. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,768 Migration script to add 'pid' and 'socket' columns to the transfer_job table.
  520. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,768
  521. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,768
  522. galaxy.model.migrate.check INFO 2011-06-16 11:20:52,768 Migrating 72 -> 73...
  523. 0073_add_ldda_to_implicit_conversion_table DEBUG 2011-06-16 11:20:53,151 Adding ldda_parent_id column to implicitly_converted_dataset_association table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  524. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,184
  525. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,184 Migration script to add 'ldda_parent_id' column to the implicitly_converted_dataset_association table.
  526. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,185
  527. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,185 Adding ldda_parent_id column to implicitly_converted_dataset_association table failed: SQLite does not support ALTER TABLE ADD FOREIGN KEY; see http://www.sqlite.org/lang_altertable.html
  528. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,185
  529. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,185 Migrating 73 -> 74...
  530. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,433
  531. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,433 Migration script to add 'purged' column to the library_dataset table.
  532. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,433
  533. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,433
  534. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,433 Migrating 74 -> 75...
  535. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,595
  536. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,595 Migration script to add a 'subindex' column to the run table.
  537. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,595
  538. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,595
  539. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,595 Migrating 75 -> 76...
  540. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,752
  541. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,753 This migration script fixes the data corruption caused in the form_values
  542. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,753 table (content json field) by migrate script 65.
  543. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,753
  544. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,753 No corrupted rows found.
  545. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,753
  546. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,753 Migrating 76 -> 77...
  547. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,962
  548. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,962 Migration script to create table for storing tool tag associations.
  549. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,962
  550. galaxy.model.migrate.check INFO 2011-06-16 11:20:53,962
  551. galaxy.model.custom_types DEBUG 2011-06-16 11:20:53,968 pysqlite>=2 egg successfully loaded for sqlite dialect
  552. galaxy.tools.data DEBUG 2011-06-16 11:20:54,008 Loaded tool data table 'all_fasta
  553. galaxy.tools.data DEBUG 2011-06-16 11:20:54,009 Loaded tool data table 'bfast_indexes
  554. galaxy.tools.data DEBUG 2011-06-16 11:20:54,009 Loaded tool data table 'blastdb
  555. galaxy.tools.data DEBUG 2011-06-16 11:20:54,010 Loaded tool data table 'blastdb_p
  556. galaxy.tools.data DEBUG 2011-06-16 11:20:54,040 Loaded tool data table 'bowtie_indexes
  557. galaxy.tools.data DEBUG 2011-06-16 11:20:54,059 Loaded tool data table 'bowtie_indexes_color
  558. galaxy.tools.data DEBUG 2011-06-16 11:20:54,090 Loaded tool data table 'bwa_indexes
  559. galaxy.tools.data DEBUG 2011-06-16 11:20:54,090 Loaded tool data table 'bwa_indexes_color
  560. galaxy.tools.data DEBUG 2011-06-16 11:20:54,169 Loaded tool data table 'indexed_maf_files
  561. galaxy.tools.data DEBUG 2011-06-16 11:20:54,169 Loaded tool data table 'ngs_sim_fasta
  562. galaxy.tools.data DEBUG 2011-06-16 11:20:54,170 Loaded tool data table 'lastz_seqs
  563. galaxy.tools.data DEBUG 2011-06-16 11:20:54,190 Loaded tool data table 'perm_base_indexes
  564. galaxy.tools.data DEBUG 2011-06-16 11:20:54,191 Loaded tool data table 'perm_color_indexes
  565. galaxy.tools.data DEBUG 2011-06-16 11:20:54,200 Loaded tool data table 'picard_indexes
  566. galaxy.tools.data DEBUG 2011-06-16 11:20:54,200 Loaded tool data table 'srma_indexes
  567. galaxy.tools.data DEBUG 2011-06-16 11:20:54,200 Loaded tool data table 'tophat_indexes
  568. galaxy.tools.data DEBUG 2011-06-16 11:20:54,201 Loaded tool data table 'ccat_configurations
  569. galaxy.tools.data DEBUG 2011-06-16 11:20:54,201 Loaded tool data table 'mosaik_indexes
  570. galaxy.tools INFO 2011-06-16 11:20:54,201 parsing the tool configuration
  571. galaxy.tools DEBUG 2011-06-16 11:20:54,230 Loading section: Get Data
  572. galaxy.tools DEBUG 2011-06-16 11:20:54,499 Loaded tool: upload1 1.1.2
  573. galaxy.tools DEBUG 2011-06-16 11:20:54,501 Loaded tool: ucsc_table_direct1 1.0.0
  574. galaxy.tools DEBUG 2011-06-16 11:20:54,504 Loaded tool: ucsc_table_direct_test1 1.0.0
  575. galaxy.tools DEBUG 2011-06-16 11:20:54,506 Loaded tool: ucsc_table_direct_archaea1 1.0.0
  576. galaxy.tools DEBUG 2011-06-16 11:20:54,508 Loaded tool: bx_browser 1.0.0
  577. galaxy.tools DEBUG 2011-06-16 11:20:54,537 Loaded tool: microbial_import1 1.0.0
  578. galaxy.tools DEBUG 2011-06-16 11:20:54,539 Loaded tool: biomart 1.0.1
  579. galaxy.tools DEBUG 2011-06-16 11:20:54,546 Loaded tool: biomart_test 1.0.1
  580. galaxy.tools DEBUG 2011-06-16 11:20:54,548 Loaded tool: cbi_rice_mart 1.0.1
  581. galaxy.tools DEBUG 2011-06-16 11:20:54,550 Loaded tool: gramenemart 1.0.1
  582. galaxy.tools DEBUG 2011-06-16 11:20:54,552 Loaded tool: modENCODEfly 1.0.0
  583. galaxy.tools DEBUG 2011-06-16 11:20:54,582 Loaded tool: flymine 1.0.0
  584. galaxy.tools DEBUG 2011-06-16 11:20:54,584 Loaded tool: flymine_test 1.0.0
  585. galaxy.tools DEBUG 2011-06-16 11:20:54,585 Loaded tool: modmine 1.0.0
  586. galaxy.tools DEBUG 2011-06-16 11:20:54,587 Loaded tool: ratmine 1.0.0
  587. galaxy.tools DEBUG 2011-06-16 11:20:54,588 Loaded tool: yeastmine 1.0.0
  588. galaxy.tools DEBUG 2011-06-16 11:20:54,589 Loaded tool: metabolicmine 1.0.0
  589. galaxy.tools DEBUG 2011-06-16 11:20:54,591 Loaded tool: modENCODEworm 1.0.0
  590. galaxy.tools DEBUG 2011-06-16 11:20:54,593 Loaded tool: wormbase 1.0.0
  591. galaxy.tools DEBUG 2011-06-16 11:20:54,595 Loaded tool: wormbase_test 1.0.0
  592. galaxy.tools DEBUG 2011-06-16 11:20:54,597 Loaded tool: eupathdb 1.0.0
  593. galaxy.tools DEBUG 2011-06-16 11:20:54,598 Loaded tool: encode_db1 1.0.0
  594. galaxy.tools DEBUG 2011-06-16 11:20:54,600 Loaded tool: epigraph_import 1.0.0
  595. galaxy.tools DEBUG 2011-06-16 11:20:54,602 Loaded tool: epigraph_import_test 1.0.0
  596. galaxy.tools DEBUG 2011-06-16 11:20:54,605 Loaded tool: hbvar 1.0.0
  597. galaxy.tools DEBUG 2011-06-16 11:20:54,640 Loaded tool: fix_errors 1.0.0
  598. galaxy.tools DEBUG 2011-06-16 11:20:54,640 Loading section: Send Data
  599. galaxy.tools DEBUG 2011-06-16 11:20:54,656 Loaded tool: epigraph_export 1.0.0
  600. galaxy.tools DEBUG 2011-06-16 11:20:54,671 Loaded tool: epigraph_test_export 1.0.0
  601. galaxy.tools DEBUG 2011-06-16 11:20:54,671 Loading section: ENCODE Tools
  602. galaxy.tools DEBUG 2011-06-16 11:20:54,712 Loaded tool: gencode_partition1 1.0.0
  603. galaxy.tools DEBUG 2011-06-16 11:20:54,732 Loaded tool: random_intervals1 1.0.0
  604. galaxy.tools DEBUG 2011-06-16 11:20:54,732 Loading section: Lift-Over
  605. galaxy.tools DEBUG 2011-06-16 11:20:54,748 Loaded tool: liftOver1 1.0.2
  606. galaxy.tools DEBUG 2011-06-16 11:20:54,748 Loading section: Text Manipulation
  607. galaxy.tools DEBUG 2011-06-16 11:20:54,764 Loaded tool: addValue 1.0.0
  608. galaxy.tools DEBUG 2011-06-16 11:20:54,780 Loaded tool: Add_a_column1 1.1.0
  609. galaxy.tools DEBUG 2011-06-16 11:20:54,852 Loaded tool: cat1 1.0.0
  610. galaxy.tools DEBUG 2011-06-16 11:20:54,875 Loaded tool: Cut1 1.0.1
  611. galaxy.tools DEBUG 2011-06-16 11:20:54,890 Loaded tool: mergeCols1 1.0.1
  612. galaxy.tools DEBUG 2011-06-16 11:20:54,901 Loaded tool: Convert characters1 1.0.0
  613. galaxy.tools DEBUG 2011-06-16 11:20:54,927 Loaded tool: createInterval 1.0.0
  614. galaxy.tools DEBUG 2011-06-16 11:20:54,961 Loaded tool: Cut1 1.0.1
  615. galaxy.tools DEBUG 2011-06-16 11:20:54,979 Loaded tool: ChangeCase 1.0.0
  616. galaxy.tools DEBUG 2011-06-16 11:20:55,229 Loaded tool: Paste1 1.0.0
  617. galaxy.tools DEBUG 2011-06-16 11:20:55,251 Loaded tool: Remove beginning1 1.0.0
  618. galaxy.tools DEBUG 2011-06-16 11:20:55,259 Loaded tool: random_lines1 1.0.0
  619. galaxy.tools DEBUG 2011-06-16 11:20:55,268 Loaded tool: Show beginning1 1.0.0
  620. galaxy.tools DEBUG 2011-06-16 11:20:55,278 Loaded tool: Show tail1 1.0.0
  621. galaxy.tools DEBUG 2011-06-16 11:20:55,295 Loaded tool: trimmer 0.0.1
  622. galaxy.tools DEBUG 2011-06-16 11:20:55,305 Loaded tool: wc_gnu 1.0.0
  623. galaxy.tools DEBUG 2011-06-16 11:20:55,335 Loaded tool: dna_filter 1.0.0
  624. galaxy.tools DEBUG 2011-06-16 11:20:55,410 Loaded tool: tables_arithmetic_operations 1.0.0
  625. galaxy.tools DEBUG 2011-06-16 11:20:55,411 Loading section: Filter and Sort
  626. galaxy.tools DEBUG 2011-06-16 11:20:55,439 Loaded tool: Filter1 1.0.1
  627. galaxy.tools DEBUG 2011-06-16 11:20:55,455 Loaded tool: sort1 1.0.1
  628. galaxy.tools DEBUG 2011-06-16 11:20:55,487 Loaded tool: Grep1 1.0.1
  629. galaxy.tools DEBUG 2011-06-16 11:20:55,501 Loaded tool: Extract_features1 1.0.0
  630. galaxy.tools DEBUG 2011-06-16 11:20:55,520 Loaded tool: gff_filter_by_attribute 0.1
  631. galaxy.tools DEBUG 2011-06-16 11:20:55,534 Loaded tool: gff_filter_by_feature_count 0.1
  632. galaxy.tools DEBUG 2011-06-16 11:20:55,542 Loaded tool: gtf_filter_by_attribute_values_list 0.1
  633. galaxy.tools DEBUG 2011-06-16 11:20:55,542 Loading section: Join, Subtract and Group
  634. galaxy.tools DEBUG 2011-06-16 11:20:55,564 Loaded tool: join1 2.0.2
  635. galaxy.tools DEBUG 2011-06-16 11:20:55,600 Loaded tool: comp1 1.0.2
  636. galaxy.tools DEBUG 2011-06-16 11:20:55,620 Loaded tool: subtract_query1 1.0.0
  637. galaxy.tools DEBUG 2011-06-16 11:20:55,638 Loaded tool: Grouping1 1.9.4
  638. galaxy.tools DEBUG 2011-06-16 11:20:55,666 Loaded tool: column_join 1.1.0
  639. galaxy.tools DEBUG 2011-06-16 11:20:55,666 Loading section: Convert Formats
  640. galaxy.tools DEBUG 2011-06-16 11:20:55,687 Loaded tool: axt_to_concat_fasta 1.0.0
  641. galaxy.tools DEBUG 2011-06-16 11:20:55,707 Loaded tool: axt_to_fasta 1.0.0
  642. galaxy.tools DEBUG 2011-06-16 11:20:55,731 Loaded tool: axt_to_lav_1 1.0.0
  643. galaxy.tools DEBUG 2011-06-16 11:20:55,744 Loaded tool: bed2gff1 2.0.0
  644. galaxy.tools DEBUG 2011-06-16 11:20:55,781 Loaded tool: fasta2tab 1.1.0
  645. galaxy.tools DEBUG 2011-06-16 11:20:55,794 Loaded tool: gff2bed1 1.0.1
  646. galaxy.tools DEBUG 2011-06-16 11:20:55,831 Loaded tool: lav_to_bed1 1.0.0
  647. galaxy.tools DEBUG 2011-06-16 11:20:55,901 Loaded tool: MAF_To_BED1 1.0.0
  648. galaxy.tools DEBUG 2011-06-16 11:20:55,932 Loaded tool: MAF_To_Interval1 1.0.0
  649. galaxy.tools DEBUG 2011-06-16 11:20:55,967 Loaded tool: MAF_To_Fasta1 1.0.1
  650. galaxy.tools DEBUG 2011-06-16 11:20:55,987 Loaded tool: tab2fasta 1.1.0
  651. galaxy.tools DEBUG 2011-06-16 11:20:55,994 Loaded tool: fastq_to_fasta_python 1.0.0
  652. galaxy.tools DEBUG 2011-06-16 11:20:56,012 Loaded tool: wiggle2simple1 1.0.0
  653. galaxy.tools DEBUG 2011-06-16 11:20:56,034 Loaded tool: Sff_extractor 1.0.0
  654. galaxy.tools DEBUG 2011-06-16 11:20:56,052 Loaded tool: gtf2bedgraph 1.0.0
  655. galaxy.tools DEBUG 2011-06-16 11:20:56,069 Loaded tool: wig_to_bigWig 1.1.0
  656. galaxy.tools DEBUG 2011-06-16 11:20:56,077 Loaded tool: bed_to_bigBed 1.0.0
  657. galaxy.tools DEBUG 2011-06-16 11:20:56,077 Loading section: Extract Features
  658. galaxy.tools DEBUG 2011-06-16 11:20:56,092 Loaded tool: gene2exon1 1.0.0
  659. galaxy.tools DEBUG 2011-06-16 11:20:56,092 Loading section: Fetch Sequences
  660. galaxy.tools DEBUG 2011-06-16 11:20:56,118 Loaded tool: Extract genomic DNA 1 2.2.1
  661. galaxy.tools DEBUG 2011-06-16 11:20:56,118 Loading section: Fetch Alignments
  662. galaxy.tools DEBUG 2011-06-16 11:20:56,159 Loaded tool: Interval2Maf_pairwise1 1.0.1
  663. galaxy.tools DEBUG 2011-06-16 11:20:56,198 Loaded tool: Interval2Maf1 1.0.1
  664. galaxy.tools DEBUG 2011-06-16 11:20:56,224 Loaded tool: MAF_split_blocks_by_species1 1.0.0
  665. galaxy.tools DEBUG 2011-06-16 11:20:56,241 Loaded tool: Interval_Maf_Merged_Fasta2 1.0.1
  666. galaxy.tools DEBUG 2011-06-16 11:20:56,298 Loaded tool: GeneBed_Maf_Fasta2 1.0.1
  667. galaxy.tools DEBUG 2011-06-16 11:20:56,318 Loaded tool: maf_stats1 1.0.1
  668. galaxy.tools DEBUG 2011-06-16 11:20:56,327 Loaded tool: MAF_Thread_For_Species1 1.0.0
  669. galaxy.tools DEBUG 2011-06-16 11:20:56,338 Loaded tool: MAF_Limit_To_Species1 1.0.0
  670. galaxy.tools DEBUG 2011-06-16 11:20:56,346 Loaded tool: maf_limit_size1 1.0.1
  671. galaxy.tools DEBUG 2011-06-16 11:20:56,354 Loaded tool: maf_by_block_number1 1.0.1
  672. galaxy.tools DEBUG 2011-06-16 11:20:56,362 Loaded tool: MAF_Reverse_Complement_1 1.0.1
  673. galaxy.tools DEBUG 2011-06-16 11:20:56,388 Loaded tool: MAF_filter 1.0.1
  674. galaxy.tools DEBUG 2011-06-16 11:20:56,388 Loading section: Get Genomic Scores
  675. galaxy.tools DEBUG 2011-06-16 11:20:56,408 Loaded tool: wiggle2simple1 1.0.0
  676. galaxy.tools DEBUG 2011-06-16 11:20:56,470 Loaded tool: aggregate_scores_in_intervals2 1.1.2
  677. galaxy.tools DEBUG 2011-06-16 11:20:56,512 Loaded tool: phastOdds_for_intervals 1.0.0
  678. galaxy.tools DEBUG 2011-06-16 11:20:56,512 Loading section: Operate on Genomic Intervals
  679. galaxy.tools DEBUG 2011-06-16 11:20:56,533 Loaded tool: gops_intersect_1 1.0.0
  680. galaxy.tools DEBUG 2011-06-16 11:20:56,553 Loaded tool: gops_subtract_1 1.0.0
  681. galaxy.tools DEBUG 2011-06-16 11:20:56,568 Loaded tool: gops_merge_1 1.0.0
  682. galaxy.tools DEBUG 2011-06-16 11:20:56,585 Loaded tool: gops_concat_1 1.0.0
  683. galaxy.tools DEBUG 2011-06-16 11:20:56,613 Loaded tool: gops_basecoverage_1 1.0.0
  684. galaxy.tools DEBUG 2011-06-16 11:20:56,630 Loaded tool: gops_coverage_1 1.0.0
  685. galaxy.tools DEBUG 2011-06-16 11:20:56,647 Loaded tool: gops_complement_1 1.0.0
  686. galaxy.tools DEBUG 2011-06-16 11:20:56,668 Loaded tool: gops_cluster_1 1.0.0
  687. galaxy.tools DEBUG 2011-06-16 11:20:56,717 Loaded tool: gops_join_1 1.0.0
  688. galaxy.tools DEBUG 2011-06-16 11:20:56,768 Loaded tool: get_flanks1 1.0.0
  689. galaxy.tools DEBUG 2011-06-16 11:20:56,790 Loaded tool: flanking_features_1 4.0.1
  690. galaxy.tools DEBUG 2011-06-16 11:20:56,846 Loaded tool: Annotation_Profiler_0 1.0.0
  691. galaxy.tools DEBUG 2011-06-16 11:20:56,846 Loading section: Statistics
  692. galaxy.tools DEBUG 2011-06-16 11:20:56,872 Loaded tool: Summary_Statistics1 1.1.0
  693. galaxy.tools DEBUG 2011-06-16 11:20:56,888 Loaded tool: Count1 1.0.0
  694. galaxy.tools DEBUG 2011-06-16 11:20:56,914 Loaded tool: cor2 1.0.0
  695. galaxy.tools DEBUG 2011-06-16 11:20:56,932 Loaded tool: generate_matrix_for_pca_and_lda1 1.0.0
  696. galaxy.tools DEBUG 2011-06-16 11:20:56,957 Loaded tool: lda_analy1 1.0.1
  697. galaxy.tools DEBUG 2011-06-16 11:20:56,971 Loaded tool: plot_for_lda_output1 1.0.1
  698. galaxy.tools DEBUG 2011-06-16 11:20:57,009 Loaded tool: t_test_two_samples 1.0.0
  699. galaxy.tools DEBUG 2011-06-16 11:20:57,059 Loaded tool: compute_q_values 1.0.1
  700. galaxy.tools DEBUG 2011-06-16 11:20:57,066 Loaded tool: count_gff_features 0.1
  701. galaxy.tools DEBUG 2011-06-16 11:20:57,066 Loading section: Graph/Display Data
  702. galaxy.tools DEBUG 2011-06-16 11:20:57,088 Loaded tool: histogram_rpy 1.0.3
  703. galaxy.tools DEBUG 2011-06-16 11:20:57,107 Loaded tool: scatterplot_rpy 1.0.0
  704. galaxy.tools DEBUG 2011-06-16 11:20:57,385 Loaded tool: barchart_gnuplot 1.0.0
  705. galaxy.tools DEBUG 2011-06-16 11:20:57,404 Loaded tool: XY_Plot_1 1.0.1
  706. galaxy.tools DEBUG 2011-06-16 11:20:57,422 Loaded tool: qual_stats_boxplot 1.0.0
  707. galaxy.tools DEBUG 2011-06-16 11:20:57,442 Loaded tool: gmaj_1 2.0.1
  708. galaxy.tools DEBUG 2011-06-16 11:20:57,454 Loaded tool: laj_1 1.0.0
  709. galaxy.tools DEBUG 2011-06-16 11:20:57,467 Loaded tool: build_ucsc_custom_track_1 1.0.0
  710. galaxy.tools DEBUG 2011-06-16 11:20:57,479 Loaded tool: vcf_to_maf_customtrack1 1.0.0
  711. galaxy.tools DEBUG 2011-06-16 11:20:57,494 Loaded tool: mutation_visualize 1.0.0
  712. galaxy.tools DEBUG 2011-06-16 11:20:57,494 Loading section: Regional Variation
  713. galaxy.tools DEBUG 2011-06-16 11:20:57,514 Loaded tool: winSplitter 1.0.0
  714. galaxy.tools DEBUG 2011-06-16 11:20:57,535 Loaded tool: featureCoverage1 2.0.0
  715. galaxy.tools DEBUG 2011-06-16 11:20:57,553 Loaded tool: qualityFilter 1.0.1
  716. galaxy.tools DEBUG 2011-06-16 11:20:57,568 Loaded tool: cpgFilter 1.0.0
  717. galaxy.tools DEBUG 2011-06-16 11:20:57,582 Loaded tool: getIndels_2way 1.0.0
  718. galaxy.tools DEBUG 2011-06-16 11:20:57,594 Loaded tool: indels_3way 1.0.3
  719. galaxy.tools DEBUG 2011-06-16 11:20:57,606 Loaded tool: indelRates_3way 1.0.0
  720. galaxy.tools DEBUG 2011-06-16 11:20:57,635 Loaded tool: substitutions1 1.0.0
  721. galaxy.tools DEBUG 2011-06-16 11:20:57,649 Loaded tool: subRate1 1.0.0
  722. galaxy.tools DEBUG 2011-06-16 11:20:57,666 Loaded tool: microsats_align1 1.0.0
  723. galaxy.tools DEBUG 2011-06-16 11:20:57,682 Loaded tool: microsats_mutability1 1.1.0
  724. galaxy.tools DEBUG 2011-06-16 11:20:57,697 Loaded tool: delete_overlapping_indels 1.0.0
  725. galaxy.tools DEBUG 2011-06-16 11:20:57,727 Loaded tool: compute_motifs_frequency 1.0.0
  726. galaxy.tools DEBUG 2011-06-16 11:20:57,749 Loaded tool: compute_motif_frequencies_for_all_motifs 1.0.0
  727. galaxy.tools DEBUG 2011-06-16 11:20:57,764 Loaded tool: categorize_elements_satisfying_criteria 1.0.0
  728. galaxy.tools DEBUG 2011-06-16 11:20:57,778 Loaded tool: draw_stacked_barplots 1.0.0
  729. galaxy.tools DEBUG 2011-06-16 11:20:57,787 Loaded tool: multispecies_orthologous_microsats 1.0.1
  730. galaxy.tools DEBUG 2011-06-16 11:20:57,797 Loaded tool: microsatellite_birthdeath 1.0.0
  731. galaxy.tools DEBUG 2011-06-16 11:20:57,797 Loading section: Multiple regression
  732. galaxy.tools DEBUG 2011-06-16 11:20:57,817 Loaded tool: LinearRegression1 1.0.1
  733. galaxy.tools DEBUG 2011-06-16 11:20:57,840 Loaded tool: BestSubsetsRegression1 1.0.0
  734. galaxy.tools DEBUG 2011-06-16 11:20:57,871 Loaded tool: rcve1 1.0.0
  735. galaxy.tools DEBUG 2011-06-16 11:20:57,871 Loading section: Multivariate Analysis
  736. galaxy.tools DEBUG 2011-06-16 11:20:57,891 Loaded tool: pca1 1.0.1
  737. galaxy.tools DEBUG 2011-06-16 11:20:57,926 Loaded tool: cca1 1.0.0
  738. galaxy.tools DEBUG 2011-06-16 11:20:57,943 Loaded tool: kpca1 1.0.0
  739. galaxy.tools DEBUG 2011-06-16 11:20:57,959 Loaded tool: kcca1 1.0.0
  740. galaxy.tools DEBUG 2011-06-16 11:20:57,959 Loading section: Evolution
  741. galaxy.tools DEBUG 2011-06-16 11:20:57,971 Loaded tool: hyphy_branch_lengths_wrapper1 1.0.0
  742. galaxy.tools DEBUG 2011-06-16 11:20:57,980 Loaded tool: hyphy_nj_tree_wrapper1 1.0.0
  743. galaxy.tools DEBUG 2011-06-16 11:20:57,997 Loaded tool: hyphy_dnds_wrapper1 1.0.0
  744. galaxy.tools DEBUG 2011-06-16 11:20:58,016 Loaded tool: mutate_snp_codon_1 1.0.0
  745. galaxy.tools DEBUG 2011-06-16 11:20:58,037 Loaded tool: hgv_codingSnps 1.0.0
  746. galaxy.tools DEBUG 2011-06-16 11:20:58,054 Loaded tool: hgv_add_scores 1.0.0
  747. galaxy.tools DEBUG 2011-06-16 11:20:58,054 Loading section: Motif Tools
  748. galaxy.tools DEBUG 2011-06-16 11:20:58,081 Loaded tool: meme_meme 1.0.0
  749. galaxy.tools DEBUG 2011-06-16 11:20:58,124 Loaded tool: rgweblogo3 0.2
  750. galaxy.tools DEBUG 2011-06-16 11:20:58,124 Loading section: Multiple Alignments
  751. galaxy.tools DEBUG 2011-06-16 11:20:58,145 Loaded tool: clustalw 0.1
  752. galaxy.tools DEBUG 2011-06-16 11:20:58,145 Loading section: Metagenomic analyses
  753. galaxy.tools DEBUG 2011-06-16 11:20:58,163 Loaded tool: Fetch Taxonomic Ranks 1.1.0
  754. galaxy.tools DEBUG 2011-06-16 11:20:58,178 Loaded tool: t2t_report 1.0.0
  755. galaxy.tools DEBUG 2011-06-16 11:20:58,212 Loaded tool: Draw_phylogram 1.0.0
  756. galaxy.tools DEBUG 2011-06-16 11:20:58,232 Loaded tool: find_diag_hits 1.0.0
  757. galaxy.tools DEBUG 2011-06-16 11:20:58,249 Loaded tool: lca1 1.0.1
  758. galaxy.tools DEBUG 2011-06-16 11:20:58,274 Loaded tool: poisson2test 1.0.0
  759. galaxy.tools DEBUG 2011-06-16 11:20:58,274 Loading section: FASTA manipulation
  760. galaxy.tools DEBUG 2011-06-16 11:20:58,284 Loaded tool: fasta_compute_length 1.0.0
  761. galaxy.tools DEBUG 2011-06-16 11:20:58,296 Loaded tool: fasta_filter_by_length 1.1
  762. galaxy.tools DEBUG 2011-06-16 11:20:58,342 Loaded tool: fasta_concatenate0 0.0.0
  763. galaxy.tools DEBUG 2011-06-16 11:20:58,381 Loaded tool: fasta2tab 1.1.0
  764. galaxy.tools DEBUG 2011-06-16 11:20:58,391 Loaded tool: tab2fasta 1.1.0
  765. galaxy.tools DEBUG 2011-06-16 11:20:58,413 Loaded tool: cshl_fasta_formatter 1.0.0
  766. galaxy.tools DEBUG 2011-06-16 11:20:58,423 Loaded tool: cshl_fasta_nucleotides_changer 1.0.0
  767. galaxy.tools DEBUG 2011-06-16 11:20:58,434 Loaded tool: cshl_fastx_collapser 1.0.0
  768. galaxy.tools DEBUG 2011-06-16 11:20:58,434 Loading section: NCBI BLAST+
  769. galaxy.tools DEBUG 2011-06-16 11:20:58,484 Loaded tool: ncbi_blastn_wrapper 0.0.10
  770. galaxy.tools DEBUG 2011-06-16 11:20:58,540 Loaded tool: ncbi_blastp_wrapper 0.0.10
  771. galaxy.tools DEBUG 2011-06-16 11:20:58,595 Loaded tool: ncbi_blastx_wrapper 0.0.10
  772. galaxy.tools DEBUG 2011-06-16 11:20:58,684 Loaded tool: ncbi_tblastn_wrapper 0.0.10
  773. galaxy.tools DEBUG 2011-06-16 11:20:58,746 Loaded tool: ncbi_tblastx_wrapper 0.0.10
  774. galaxy.tools DEBUG 2011-06-16 11:20:58,815 Loaded tool: blastxml_to_tabular 0.0.8
  775. galaxy.tools DEBUG 2011-06-16 11:20:58,815 Loading section: NGS: QC and manipulation
  776. galaxy.tools DEBUG 2011-06-16 11:20:58,841 Loaded tool: fastqc 0.1
  777. galaxy.tools DEBUG 2011-06-16 11:20:58,868 Loaded tool: fastq_groomer 1.0.3
  778. galaxy.tools DEBUG 2011-06-16 11:20:58,877 Loaded tool: fastq_paired_end_splitter 1.0.0
  779. galaxy.tools DEBUG 2011-06-16 11:20:58,888 Loaded tool: fastq_paired_end_joiner 1.0.0
  780. galaxy.tools DEBUG 2011-06-16 11:20:58,910 Loaded tool: fastq_stats 1.0.0
  781. galaxy.tools DEBUG 2011-06-16 11:20:58,928 Loaded tool: quality_score_distribution 1.0.2
  782. galaxy.tools DEBUG 2011-06-16 11:20:58,942 Loaded tool: trim_reads 1.0.0
  783. galaxy.tools DEBUG 2011-06-16 11:20:58,952 Loaded tool: fastq_combiner 1.0.1
  784. galaxy.tools DEBUG 2011-06-16 11:20:58,990 Loaded tool: solid2fastq 1.0.0
  785. galaxy.tools DEBUG 2011-06-16 11:20:59,012 Loaded tool: solid_qual_stats 1.0.0
  786. galaxy.tools DEBUG 2011-06-16 11:20:59,028 Loaded tool: solid_qual_boxplot 1.0.0
  787. galaxy.tools DEBUG 2011-06-16 11:20:59,056 Loaded tool: fastq_filter 1.0.0
  788. galaxy.tools DEBUG 2011-06-16 11:20:59,069 Loaded tool: fastq_trimmer 1.0.0
  789. galaxy.tools DEBUG 2011-06-16 11:20:59,083 Loaded tool: fastq_quality_trimmer 1.0.0
  790. galaxy.tools DEBUG 2011-06-16 11:20:59,091 Loaded tool: fastq_masker_by_quality 1.0.0
  791. galaxy.tools DEBUG 2011-06-16 11:20:59,126 Loaded tool: fastq_manipulation 1.0.1
  792. galaxy.tools DEBUG 2011-06-16 11:20:59,132 Loaded tool: fastq_to_fasta_python 1.0.0
  793. galaxy.tools DEBUG 2011-06-16 11:20:59,413 Loaded tool: fastq_to_tabular 1.1.0
  794. galaxy.tools DEBUG 2011-06-16 11:20:59,421 Loaded tool: tabular_to_fastq 1.0.0
  795. galaxy.tools DEBUG 2011-06-16 11:20:59,434 Loaded tool: cshl_fastq_quality_converter 1.0.0
  796. galaxy.tools DEBUG 2011-06-16 11:20:59,456 Loaded tool: cshl_fastx_quality_statistics 1.0.0
  797. galaxy.tools DEBUG 2011-06-16 11:20:59,476 Loaded tool: cshl_fastq_quality_boxplot 1.0.0
  798. galaxy.tools DEBUG 2011-06-16 11:20:59,574 Loaded tool: cshl_fastx_nucleotides_distribution 1.0.0
  799. galaxy.tools DEBUG 2011-06-16 11:20:59,586 Loaded tool: cshl_fastq_to_fasta 1.0.0
  800. galaxy.tools DEBUG 2011-06-16 11:20:59,603 Loaded tool: cshl_fastq_quality_filter 1.0.0
  801. galaxy.tools DEBUG 2011-06-16 11:20:59,618 Loaded tool: cshl_fastq_to_fasta 1.0.0
  802. galaxy.tools DEBUG 2011-06-16 11:20:59,633 Loaded tool: cshl_fastx_artifacts_filter 1.0.0
  803. galaxy.tools DEBUG 2011-06-16 11:20:59,651 Loaded tool: cshl_fastx_barcode_splitter 1.0.0
  804. galaxy.tools DEBUG 2011-06-16 11:20:59,691 Loaded tool: cshl_fastx_clipper 1.0.1
  805. galaxy.tools DEBUG 2011-06-16 11:20:59,702 Loaded tool: cshl_fastx_collapser 1.0.0
  806. galaxy.tools DEBUG 2011-06-16 11:20:59,715 Loaded tool: cshl_fastx_renamer 0.0.11
  807. galaxy.tools DEBUG 2011-06-16 11:20:59,735 Loaded tool: cshl_fastx_reverse_complement 1.0.0
  808. galaxy.tools DEBUG 2011-06-16 11:20:59,747 Loaded tool: cshl_fastx_trimmer 1.0.0
  809. galaxy.tools DEBUG 2011-06-16 11:20:59,747 Loading section: NGS: Picard (beta)
  810. galaxy.tools DEBUG 2011-06-16 11:20:59,765 Loaded tool: picard_BamIndexStats 0.2.0
  811. galaxy.tools DEBUG 2011-06-16 11:20:59,872 Loaded tool: PicardASMetrics 0.03
  812. galaxy.tools DEBUG 2011-06-16 11:20:59,916 Loaded tool: PicardGCBiasMetrics 0.01
  813. galaxy.tools DEBUG 2011-06-16 11:20:59,948 Loaded tool: rgEstLibComp 0.01
  814. galaxy.tools DEBUG 2011-06-16 11:20:59,977 Loaded tool: PicardInsertSize 0.3.0
  815. galaxy.tools DEBUG 2011-06-16 11:21:00,032 Loaded tool: PicardHsMetrics 0.01
  816. galaxy.tools DEBUG 2011-06-16 11:21:00,054 Loaded tool: picard_ARRG 0.2.0
  817. galaxy.tools DEBUG 2011-06-16 11:21:00,075 Loaded tool: picard_ReorderSam 0.3.0
  818. galaxy.tools DEBUG 2011-06-16 11:21:00,092 Loaded tool: picard_ReplaceSamHeader 0.2.0
  819. galaxy.tools DEBUG 2011-06-16 11:21:00,125 Loaded tool: rgPicFixMate 0.2.0
  820. galaxy.tools DEBUG 2011-06-16 11:21:00,159 Loaded tool: rgPicardMarkDups 0.01
  821. galaxy.tools DEBUG 2011-06-16 11:21:00,159 Loading section: NGS: Mapping
  822. galaxy.tools DEBUG 2011-06-16 11:21:00,194 Loaded tool: lastz_wrapper_2 1.2.2
  823. galaxy.tools DEBUG 2011-06-16 11:21:00,215 Loaded tool: lastz_paired_reads_wrapper 1.1.1
  824. galaxy.tools DEBUG 2011-06-16 11:21:00,263 Loaded tool: bowtie_wrapper 1.1.2
  825. galaxy.tools DEBUG 2011-06-16 11:21:00,305 Loaded tool: bowtie_color_wrapper 1.1.2
  826. galaxy.tools DEBUG 2011-06-16 11:21:00,336 Loaded tool: bwa_wrapper 1.2.2
  827. galaxy.tools DEBUG 2011-06-16 11:21:00,370 Loaded tool: bwa_color_wrapper 1.0.1
  828. galaxy.tools DEBUG 2011-06-16 11:21:00,398 Loaded tool: bfast_wrapper 0.1.3
  829. galaxy.tools DEBUG 2011-06-16 11:21:00,417 Loaded tool: megablast_wrapper 1.1.0
  830. galaxy.tools DEBUG 2011-06-16 11:21:00,427 Loaded tool: megablast_xml_parser 1.0.0
  831. galaxy.tools DEBUG 2011-06-16 11:21:00,458 Loaded tool: PerM 1.1.2
  832. galaxy.tools DEBUG 2011-06-16 11:21:00,505 Loaded tool: srma_wrapper 0.2.5
  833. galaxy.tools DEBUG 2011-06-16 11:21:00,515 Loaded tool: mosaik_wrapper 1.1.1
  834. galaxy.tools DEBUG 2011-06-16 11:21:00,515 Loading section: NGS: Indel Analysis
  835. galaxy.tools DEBUG 2011-06-16 11:21:00,548 Loaded tool: sam_indel_filter 1.0.0
  836. galaxy.tools DEBUG 2011-06-16 11:21:00,565 Loaded tool: indel_sam2interval 1.0.0
  837. galaxy.tools DEBUG 2011-06-16 11:21:00,577 Loaded tool: indel_table 1.0.0
  838. galaxy.tools DEBUG 2011-06-16 11:21:00,593 Loaded tool: indel_analysis 1.0.0
  839. galaxy.tools DEBUG 2011-06-16 11:21:00,594 Loading section: NGS: RNA Analysis
  840. galaxy.tools DEBUG 2011-06-16 11:21:00,639 Loaded tool: tophat 1.2.1
  841. galaxy.tools DEBUG 2011-06-16 11:21:00,665 Loaded tool: cufflinks 0.9.1
  842. galaxy.tools DEBUG 2011-06-16 11:21:00,695 Loaded tool: cuffcompare 0.9.1
  843. galaxy.tools DEBUG 2011-06-16 11:21:00,744 Loaded tool: cuffdiff 0.9.1
  844. galaxy.tools DEBUG 2011-06-16 11:21:00,752 Loaded tool: filter_combined_via_tracking 0.1
  845. galaxy.tools DEBUG 2011-06-16 11:21:00,752 Loading section: NGS: SAM Tools
  846. galaxy.tools DEBUG 2011-06-16 11:21:00,768 Loaded tool: sam_bw_filter 1.0.0
  847. galaxy.tools DEBUG 2011-06-16 11:21:00,778 Loaded tool: sam2interval 1.0.1
  848. galaxy.tools DEBUG 2011-06-16 11:21:00,809 Loaded tool: sam_to_bam 1.1.2
  849. galaxy.tools DEBUG 2011-06-16 11:21:00,818 Loaded tool: bam_to_sam 1.0.3
  850. galaxy.tools DEBUG 2011-06-16 11:21:00,827 Loaded tool: sam_merge 1.1.1
  851. galaxy.tools DEBUG 2011-06-16 11:21:00,846 Loaded tool: sam_pileup 1.1.1
  852. galaxy.tools DEBUG 2011-06-16 11:21:00,901 Loaded tool: pileup_parser 1.0.2
  853. galaxy.tools DEBUG 2011-06-16 11:21:00,962 Loaded tool: pileup_interval 1.0.0
  854. galaxy.tools DEBUG 2011-06-16 11:21:00,970 Loaded tool: samtools_flagstat 1.0.0
  855. galaxy.tools DEBUG 2011-06-16 11:21:00,971 Loading section: NGS: GATK Tools
  856. galaxy.tools DEBUG 2011-06-16 11:21:01,001 Loaded tool: gatk_realigner_target_creator 0.0.1
  857. galaxy.tools DEBUG 2011-06-16 11:21:01,026 Loaded tool: gatk_indel_realigner 0.0.1
  858. galaxy.tools DEBUG 2011-06-16 11:21:01,051 Loaded tool: gatk_count_covariates 0.0.1
  859. galaxy.tools DEBUG 2011-06-16 11:21:01,077 Loaded tool: gatk_table_recalibration 0.0.1
  860. galaxy.tools DEBUG 2011-06-16 11:21:01,090 Loaded tool: gatk_analyze_covariates 0.0.1
  861. galaxy.tools DEBUG 2011-06-16 11:21:01,112 Loaded tool: gatk_unified_genotyper 0.0.1
  862. galaxy.tools DEBUG 2011-06-16 11:21:01,112 Loading section: NGS: Peak Calling
  863. galaxy.tools DEBUG 2011-06-16 11:21:01,129 Loaded tool: peakcalling_macs 1.0.1
  864. galaxy.tools DEBUG 2011-06-16 11:21:01,140 Loaded tool: peakcalling_ccat 0.0.1
  865. galaxy.tools DEBUG 2011-06-16 11:21:01,171 Loaded tool: bed2genetrack 1.0.1
  866. galaxy.tools DEBUG 2011-06-16 11:21:01,182 Loaded tool: predict2genetrack 1.0.0
  867. galaxy.tools DEBUG 2011-06-16 11:21:01,183 Loading section: NGS: Simulation
  868. galaxy.tools DEBUG 2011-06-16 11:21:01,198 Loaded tool: ngs_simulation 1.0.0
  869. galaxy.tools DEBUG 2011-06-16 11:21:01,198 Loading section: SNP/WGA: Data; Filters
  870. galaxy.tools DEBUG 2011-06-16 11:21:01,253 Loaded tool: upload1 1.1.2
  871. galaxy.tools DEBUG 2011-06-16 11:21:01,257 Loaded tool: library_access1 1.0.0
  872. galaxy.tools DEBUG 2011-06-16 11:21:01,297 Loaded tool: rgClean1 1.0.0
  873. galaxy.tools DEBUG 2011-06-16 11:21:01,583 Loaded tool: rgPedSub1 1.0.0
  874. galaxy.tools DEBUG 2011-06-16 11:21:01,612 Loaded tool: rgLDIndep1 1.0.0
  875. galaxy.tools DEBUG 2011-06-16 11:21:01,630 Loaded tool: fakePhe1 1.0.0
  876. galaxy.tools DEBUG 2011-06-16 11:21:01,648 Loaded tool: rgfakePed1 0.02
  877. galaxy.tools DEBUG 2011-06-16 11:21:01,648 Loading section: SNP/WGA: QC; LD; Plots
  878. galaxy.tools DEBUG 2011-06-16 11:21:01,668 Loaded tool: rgQC1 1.0.0
  879. galaxy.tools DEBUG 2011-06-16 11:21:01,695 Loaded tool: rgEigPCA1 1.0.0
  880. galaxy.tools DEBUG 2011-06-16 11:21:01,715 Loaded tool: rgHaploView1 0.3
  881. galaxy.tools DEBUG 2011-06-16 11:21:01,746 Loaded tool: rgManQQ1 1.0.1
  882. galaxy.tools.test DEBUG 2011-06-16 11:21:01,765 Error in add_param for force: Unable to determine parameter type of test input 'force'. Ensure that the parameter exists and that any container groups are defined first.
  883. galaxy.tools DEBUG 2011-06-16 11:21:01,765 Loaded tool: rgGRR1 1.0.0
  884. galaxy.tools DEBUG 2011-06-16 11:21:01,765 Loading section: SNP/WGA: Statistical Models
  885. galaxy.tools DEBUG 2011-06-16 11:21:01,809 Loaded tool: rgCaCo1 1.0.0
  886. galaxy.tools DEBUG 2011-06-16 11:21:01,837 Loaded tool: rgTDT1 1.0.0
  887. galaxy.tools DEBUG 2011-06-16 11:21:01,882 Loaded tool: rgGLM1 0.2
  888. galaxy.tools DEBUG 2011-06-16 11:21:01,909 Loaded tool: rgManQQ1 1.0.1
  889. galaxy.tools DEBUG 2011-06-16 11:21:01,909 Loading section: Human Genome Variation
  890. galaxy.tools DEBUG 2011-06-16 11:21:01,929 Loaded tool: hgv_codingSnps 1.0.0
  891. galaxy.tools DEBUG 2011-06-16 11:21:01,949 Loaded tool: hgv_add_scores 1.0.0
  892. galaxy.tools DEBUG 2011-06-16 11:21:02,005 Loaded tool: hgv_sift 1.0.0
  893. galaxy.tools DEBUG 2011-06-16 11:21:02,019 Loaded tool: hgv_linkToGProfile 1.0.0
  894. galaxy.tools DEBUG 2011-06-16 11:21:02,035 Loaded tool: hgv_david 1.0.0
  895. galaxy.tools DEBUG 2011-06-16 11:21:02,064 Loaded tool: hgv_ctdBatch 1.0.0
  896. galaxy.tools DEBUG 2011-06-16 11:21:02,097 Loaded tool: hgv_funDo 1.0.0
  897. galaxy.tools DEBUG 2011-06-16 11:21:02,115 Loaded tool: hgv_snpFreq 1.0.0
  898. galaxy.tools DEBUG 2011-06-16 11:21:02,136 Loaded tool: hgv_ldtools 1.0.0
  899. galaxy.tools DEBUG 2011-06-16 11:21:02,156 Loaded tool: hgv_pass 1.0.0
  900. galaxy.tools DEBUG 2011-06-16 11:21:02,179 Loaded tool: hgv_gpass 1.0.0
  901. galaxy.tools DEBUG 2011-06-16 11:21:02,215 Loaded tool: hgv_beam 1.0.0
  902. galaxy.tools DEBUG 2011-06-16 11:21:02,242 Loaded tool: hgv_lps 1.0.0
  903. galaxy.tools DEBUG 2011-06-16 11:21:02,263 Loaded tool: hgv_hilbertvis 1.0.0
  904. galaxy.tools DEBUG 2011-06-16 11:21:02,284 Loaded tool: freebayes_wrapper 0.5.0
  905. galaxy.tools DEBUG 2011-06-16 11:21:02,284 Loading section: VCF Tools
  906. galaxy.tools DEBUG 2011-06-16 11:21:02,295 Loaded tool: vcf_intersect 1.0.0
  907. galaxy.tools DEBUG 2011-06-16 11:21:02,307 Loaded tool: vcf_annotate 1.0.0
  908. galaxy.tools DEBUG 2011-06-16 11:21:02,321 Loaded tool: vcf_filter 1.0.0
  909. galaxy.tools DEBUG 2011-06-16 11:21:02,336 Loaded tool: vcf_extract 1.0.0
  910. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,363 Loaded converter: CONVERTER_Bam_Bai_0
  911. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,369 Loaded converter: CONVERTER_bam_to_summary_tree_0
  912. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,402 Loaded converter: CONVERTER_bed_to_gff_0
  913. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,408 Loaded converter: CONVERTER_interval_to_coverage_0
  914. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,415 Loaded converter: CONVERTER_bed_to_bgzip_0
  915. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,445 Loaded converter: CONVERTER_bed_to_tabix_0
  916. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,452 Loaded converter: CONVERTER_bed_to_summary_tree_0
  917. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,458 Loaded converter: CONVERTER_bed_to_genetrack_0
  918. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,464 Loaded converter: CONVERTER_fasta_to_tabular
  919. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,470 Loaded converter: CONVERTER_fasta_to_bowtie_base_index
  920. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,476 Loaded converter: CONVERTER_fasta_to_bowtie_color_index
  921. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,482 Loaded converter: CONVERTER_gff_to_bed_0
  922. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,488 Loaded converter: CONVERTER_gff_to_interval_index_0
  923. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,497 Loaded converter: CONVERTER_gff_to_summary_tree_0
  924. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,516 Loaded converter: CONVERTER_interval_to_bed_0
  925. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,522 Loaded converter: CONVERTER_interval_to_bedstrict_0
  926. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,528 Loaded converter: CONVERTER_interval_to_bed6_0
  927. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,535 Loaded converter: CONVERTER_interval_to_bed12_0
  928. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,541 Loaded converter: CONVERTER_maf_to_fasta_0
  929. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,549 Loaded converter: CONVERTER_maf_to_interval_0
  930. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,555 Loaded converter: CONVERTER_vcf_to_bgzip_0
  931. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,583 Loaded converter: CONVERTER_vcf_to_tabix_0
  932. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,590 Loaded converter: CONVERTER_vcf_to_summary_tree_0
  933. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,596 Loaded converter: CONVERTER_wig_to_bigwig
  934. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,597 Loaded converter: CONVERTER_wiggle_to_interval_0
  935. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,603 Loaded converter: lped2fpedconvert
  936. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,609 Loaded converter: lped2pbedconvert
  937. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,620 Loaded converter: pbed2lpedconvert
  938. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,626 Loaded converter: pbed2ldindepconvert
  939. galaxy.tools.imp_exp DEBUG 2011-06-16 11:21:02,659 Loaded history export tool: __EXPORT_HISTORY__
  940. galaxy.tools.imp_exp DEBUG 2011-06-16 11:21:02,685 Loaded history import tool: __IMPORT_HISTORY__
  941. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,687 Loaded external metadata tool: __SET_METADATA__
  942. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,693 Loaded indexer: INDEXER_Coverage_0
  943. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,702 Loaded indexer: INDEXER_Coverage_0
  944. galaxy.datatypes.registry DEBUG 2011-06-16 11:21:02,708 Loaded indexer: INDEXER_Interval_0
  945. galaxy.jobs.runners.local INFO 2011-06-16 11:21:02,710 starting workers
  946. galaxy.jobs.runners.local DEBUG 2011-06-16 11:21:02,761 5 workers ready
  947. galaxy.jobs DEBUG 2011-06-16 11:21:02,761 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner
  948. galaxy.jobs INFO 2011-06-16 11:21:02,772 job manager started
  949. galaxy.jobs INFO 2011-06-16 11:21:02,831 job stopper started
  950. galaxy.sample_tracking.external_service_types DEBUG 2011-06-16 11:21:02,907 Loaded external_service_type: Simple unknown sequencer 1.0.0
  951. galaxy.sample_tracking.external_service_types DEBUG 2011-06-16 11:21:02,916 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
  952. functional_tests.py INFO 2011-06-16 11:21:02,916 Embedded Universe application started
  953. galaxy.web.framework.base DEBUG 2011-06-16 11:21:02,953 Enabling 'admin' controller, class: AdminGalaxy
  954. galaxy.web.framework.base DEBUG 2011-06-16 11:21:02,955 Enabling 'async' controller, class: ASync
  955. galaxy.model.item_attrs WARNING 2011-06-16 11:21:02,966 Max zip file size is 2GB, ZIP64 not supported
  956. galaxy.web.framework.base DEBUG 2011-06-16 11:21:02,967 Enabling 'dataset' controller, class: DatasetInterface
  957. galaxy.web.framework.base DEBUG 2011-06-16 11:21:02,968 Enabling 'error' controller, class: Error
  958. galaxy.web.framework.base DEBUG 2011-06-16 11:21:02,973 Enabling 'external_service' controller, class: ExternalService
  959. galaxy.web.framework.base DEBUG 2011-06-16 11:21:02,974 Enabling 'external_services' controller, class: ExternalServiceController
  960. galaxy.web.framework.base DEBUG 2011-06-16 11:21:02,976 Enabling 'forms' controller, class: Forms
  961. galaxy.web.framework.base DEBUG 2011-06-16 11:21:02,978 Enabling 'history' controller, class: HistoryController
  962. galaxy.web.controllers.library_common WARNING 2011-06-16 11:21:03,043 Max zip file size is 2GB, ZIP64 not supported
  963. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,043 Enabling 'library' controller, class: Library
  964. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,045 Enabling 'library_admin' controller, class: LibraryAdmin
  965. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,046 Enabling 'library_common' controller, class: LibraryCommon
  966. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,047 Enabling 'mobile' controller, class: Mobile
  967. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,049 Enabling 'page' controller, class: PageController
  968. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,051 Enabling 'request_type' controller, class: RequestType
  969. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,052 Enabling 'requests' controller, class: Requests
  970. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,090 Enabling 'requests_admin' controller, class: RequestsAdmin
  971. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,091 Enabling 'requests_common' controller, class: RequestsCommon
  972. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,093 Enabling 'root' controller, class: RootController
  973. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,094 Enabling 'tag' controller, class: TagsController
  974. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,096 Enabling 'tool_runner' controller, class: ToolRunner
  975. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,173 Enabling 'tracks' controller, class: TracksController
  976. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,175 Enabling 'ucsc_proxy' controller, class: UCSCProxy
  977. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,177 Enabling 'user' controller, class: User
  978. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,179 Enabling 'visualization' controller, class: VisualizationController
  979. galaxy.web.framework.base DEBUG 2011-06-16 11:21:03,310 Enabling 'workflow' controller, class: WorkflowController
  980. galaxy.web.buildapp DEBUG 2011-06-16 11:21:03,324 Enabling 'httpexceptions' middleware
  981. galaxy.web.buildapp DEBUG 2011-06-16 11:21:03,326 Enabling 'recursive' middleware
  982. galaxy.web.buildapp DEBUG 2011-06-16 11:21:03,810 Enabling 'error' middleware
  983. galaxy.web.buildapp DEBUG 2011-06-16 11:21:03,810 Enabling 'config' middleware
  984. galaxy.web.buildapp DEBUG 2011-06-16 11:21:03,811 Enabling 'x-forwarded-host' middleware
  985. functional_tests.py DEBUG 2011-06-16 11:21:03,811 Attempting to serve app on randomly chosen port: 8082
  986. functional_tests.py INFO 2011-06-16 11:21:04,676 Embedded web server started
  987. functional_tests.py INFO 2011-06-16 11:21:04,965 Functional tests will be run against localhost:8082
  988. nose.plugins.manager DEBUG 2011-06-16 11:21:05,133 DefaultPluginManager load plugin sqlalchemy = sqlalchemy.test.noseplugin:NoseSQLAlchemy
  989. nose.plugins.manager DEBUG 2011-06-16 11:21:05,175 DefaultPluginManager load plugin nosetestdiff = nosetestdiff.plugin:NoseTestDiff
  990. nose.plugins.manager DEBUG 2011-06-16 11:21:05,177 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML
  991. Failure: OSError (No such file /Users/user/galaxy-dist/-) ... ERROR
  992.  
  993. ======================================================================
  994. ERROR: Failure: OSError (No such file /Users/user/galaxy-dist/-)
  995. ----------------------------------------------------------------------
  996. Traceback (most recent call last):
  997.  File "/Users/user/galaxy-dist/eggs/nose-0.11.1-py2.4.egg/nose/failure.py", line 39, in runTest
  998.    raise self.exc_class(self.exc_val)
  999. OSError: No such file /Users/user/galaxy-dist/-
  1000.  
  1001. ----------------------------------------------------------------------
  1002. Ran 1 test in 0.007s
  1003.  
  1004. FAILED (errors=1)
  1005. functional_tests.py INFO 2011-06-16 11:21:05,343 Shutting down
  1006. functional_tests.py INFO 2011-06-16 11:21:05,343 Shutting down embedded web server
  1007. functional_tests.py INFO 2011-06-16 11:21:05,355 Embedded web server stopped
  1008. functional_tests.py INFO 2011-06-16 11:21:05,355 Shutting down app
  1009. galaxy.jobs INFO 2011-06-16 11:21:05,355 sending stop signal to worker thread
  1010. galaxy.jobs INFO 2011-06-16 11:21:05,355 job queue stopped
  1011. galaxy.jobs.runners.local INFO 2011-06-16 11:21:05,355 sending stop signal to worker threads
  1012. galaxy.jobs.runners.local INFO 2011-06-16 11:21:05,355 local job runner stopped
  1013. galaxy.jobs INFO 2011-06-16 11:21:05,356 sending stop signal to worker thread
  1014. galaxy.jobs INFO 2011-06-16 11:21:05,356 job stopper stopped
  1015. functional_tests.py INFO 2011-06-16 11:21:05,356 Embedded Universe application stopped
  1016. functional_tests.py INFO 2011-06-16 11:21:05,356 Cleaning up temporary files in /var/folders/gq/gquONqXXGUGk1+4cFi9O8U+++TM/-Tmp-/tmpEQ3_W-
  1017. galaxy.jobs INFO 2011-06-16 11:21:05,358 sending stop signal to worker thread
  1018. galaxy.jobs INFO 2011-06-16 11:21:05,358 job queue stopped
  1019. galaxy.jobs.runners.local INFO 2011-06-16 11:21:05,358 sending stop signal to worker threads
  1020. galaxy.jobs.runners.local INFO 2011-06-16 11:21:05,358 local job runner stopped
  1021. galaxy.jobs INFO 2011-06-16 11:21:05,358 sending stop signal to worker thread
  1022. galaxy.jobs INFO 2011-06-16 11:21:05,359 job stopper stopped
  1023. Exception exceptions.OSError: (2, 'No such file or directory', '/var/folders/gq/gquONqXXGUGk1+4cFi9O8U+++TM/-Tmp-/tmpEQ3_W-/database/tmp/tmpm9mseF') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', mode 'w' at 0xcfb4260>> ignored
  1024. 'run_functional_tests.sh help'                  for help
  1025. Note: galaxy test framework uses tool_conf.xml.sample, not tool_conf.xml
  1026. udp035588uds:galaxy-dist user$
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!