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  1. $ sh run_community.sh
  2. python path is: /home/galaxy/galaxy-dev/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs2.egg, /home/galaxy/galaxy-dev/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs2.egg, /home/galaxy/galaxy-dev/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs2.egg, /home/galaxy/galaxy-dev/eggs/amqplib-0.6.1-py2.6.egg, /home/galaxy/galaxy-dev/eggs/pexpect-2.4-py2.6.egg, /home/galaxy/galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /home/galaxy/galaxy-dev/eggs/Babel-0.9.4-py2.6.egg, /home/galaxy/galaxy-dev/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs2.egg, /home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.6.egg, /home/galaxy/galaxy-dev/eggs/WebHelpers-0.2-py2.6.egg, /home/galaxy/galaxy-dev/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg, /home/galaxy/galaxy-dev/eggs/wchartype-0.1-py2.6.egg, /home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg, /home/galaxy/galaxy-dev/eggs/docutils-0.7-py2.6.egg, /home/galaxy/galaxy-dev/eggs/WebOb-0.8.5-py2.6.egg, /home/galaxy/galaxy-dev/eggs/Routes-1.12.3-py2.6.egg, /home/galaxy/galaxy-dev/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg, /home/galaxy/galaxy-dev/eggs/PasteDeploy-1.3.3-py2.6.egg, /home/galaxy/galaxy-dev/eggs/PasteScript-1.7.3-py2.6.egg, /home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg, /home/galaxy/galaxy-dev/lib, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/ipython-0.10-py2.6.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/numpy-1.4.1-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/matplotlib-0.99.3-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/mercurial-1.5.4-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/Markdown-2.0.3-py2.6.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/scipy-0.8.0-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/BNfinder-0.3.3-py2.6.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/h5py-1.3.1-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/rpy2-2.1.9_20110406-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/Cython-0.14.1-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages/pysam-0.5-py2.6-linux-x86_64.egg, /home/galaxy/.local/lib/python2.6/site-packages/HTSeq-0.5.1p2-py2.6-linux-x86_64.egg, /home/galaxy/.local/lib/python2.6/site-packages/pysam-0.4.1-py2.6-linux-x86_64.egg, /home/galaxy/.local/lib/python2.6/site-packages/Cython-0.14.1-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/site-packages/Twisted-11.0.0-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/site-packages/zope.interface-3.6.4-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/site-packages/foolscap-0.6.1-py2.6.egg, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/site-packages/ruffus-2.2-py2.6.egg, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/site-packages/biopython-1.58-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/site-packages/HTSeq-0.5.3p3-py2.6-linux-x86_64.egg, /g/steinmetz/collaboration/software/CentOS5/lib/python2.6/site-packages, /home/galaxy/galaxy-dev, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python26.zip, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/plat-linux2, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/lib-tk, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/lib-old, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/lib-dynload, /home/galaxy/.local/lib/python2.6/site-packages, /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/site-packages
  3. galaxy.webapps.community.model.migrate.check INFO 2011-11-25 15:32:57,157 At database version 10
  4. /home/galaxy/galaxy-dev/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs2.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility
  5. from csamtools import *
  6. /home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11: DeprecationWarning: the md5 module is deprecated; use hashlib instead
  7. import md5
  8. Starting server in PID 5306.
  9. serving on http://127.0.0.1:9009
  10. 10.11.70.109 - - [25/Nov/2011:15:33:31 +0200] "GET / HTTP/1.1" 500 - "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.1 (KHTML, like Gecko) Chrome/14.0.835.186 Safari/535.1"
  11. Error - <type 'exceptions.AttributeError'>: 'Configuration' object has no attribute 'ucsc_display_sites'
  12. URL: http://taiji/
  13. File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__
  14. app_iter = self.application(environ, start_response)
  15. File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__
  16. return self.application(environ, start_response)
  17. File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__
  18. return self.application(environ, start_response)
  19. File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/base.py', line 134 in __call__
  20. trans = self.transaction_factory( environ )
  21. File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 187 in <lambda>
  22. self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) )
  23. File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 207 in transaction_chooser
  24. return GalaxyWebUITransaction( environ, galaxy_app, self, session_cookie )
  25. File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 860 in __init__
  26. self._ensure_logged_in_user( environ )
  27. File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 420 in _ensure_logged_in_user
  28. if self.app.config.ucsc_display_sites and self.request.path == display_as:
  29. AttributeError: 'Configuration' object has no attribute 'ucsc_display_sites'
  30.  
  31.  
  32. CGI Variables
  33. -------------
  34. CONTENT_LENGTH: '0'
  35. HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
  36. HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=0.7,*;q=0.3'
  37. HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
  38. HTTP_ACCEPT_LANGUAGE: 'fr-FR,fr;q=0.8,en-US;q=0.6,en;q=0.4'
  39. HTTP_AUTHORIZATION: 'Basic c2NobWl0dDpFdmE+PDIxMQ=='
  40. HTTP_CONNECTION: 'Keep-Alive'
  41. HTTP_HOST: 'taiji'
  42. HTTP_REMOTE_USER: 'schmitt'
  43. HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.1 (KHTML, like Gecko) Chrome/14.0.835.186 Safari/535.1'
  44. HTTP_X_FORWARDED_FOR: '10.11.70.109'
  45. HTTP_X_FORWARDED_HOST: 'taiji'
  46. HTTP_X_FORWARDED_SERVER: 'taiji.embl.de'
  47. ORGINAL_HTTP_HOST: 'localhost:9009'
  48. ORGINAL_REMOTE_ADDR: '127.0.0.1'
  49. PATH_INFO: '/'
  50. REMOTE_ADDR: '10.11.70.109'
  51. REQUEST_METHOD: 'GET'
  52. SERVER_NAME: '127.0.0.1'
  53. SERVER_PORT: '9009'
  54. SERVER_PROTOCOL: 'HTTP/1.1'
  55.  
  56.  
  57. Configuration
  58. -------------
  59. __file__: '/home/galaxy/galaxy-dev/community_wsgi.ini'
  60. admin_users: 'delhomme@embl.de,schmitt@embl.de,sauer@embl.de,su@embl.de,girardot@embl.de'
  61. database_connection: 'postgres://galaxy_dev:galaxy_dev@manni/galaxy_toolshed_db'
  62. debug: 'false'
  63. email_from: 'galaxy@embl.de'
  64. file_path: '/g/funcgen/toolshed/community_files'
  65. here: '/home/galaxy/galaxy-dev'
  66. id_secret: 'changethisinproductiontoo'
  67. log_level: 'INFO'
  68. new_file_path: '/tmpdata/tmp/toolshed'
  69. require_login: 'True'
  70. sendmail_path: '/usr/sbin/sendmail'
  71. session_data_dir: '/home/galaxy/galaxy-dev/database/beaker_sessions'
  72. session_key: 'galaxysessions'
  73. session_secret: 'changethisinproduction'
  74. session_type: 'memory'
  75. smtp_server: 'smtp.embl.de'
  76. static_cache_time: '360'
  77. static_dir: '/home/galaxy/galaxy-dev/static/'
  78. static_enabled: 'True'
  79. static_favicon_dir: '/home/galaxy/galaxy-dev/static/favicon.ico'
  80. static_images_dir: '/home/galaxy/galaxy-dev/static/images'
  81. static_scripts_dir: '/home/galaxy/galaxy-dev/static/scripts/'
  82. static_style_dir: '/home/galaxy/galaxy-dev/static/june_2007_style/blue'
  83. use_beaker_session: 'True'
  84. use_lint: 'false'
  85. use_new_layout: 'true'
  86.  
  87.  
  88. WSGI Variables
  89. --------------
  90. application: <paste.recursive.RecursiveMiddleware object at 0x1d092c10>
  91. paste.cookies: (<SimpleCookie: >, '')
  92. paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  93. paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x1cbd9650>
  94. paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x1a6d6a50>
  95. paste.recursive.forward: <paste.recursive.Forwarder from />
  96. paste.recursive.include: <paste.recursive.Includer from />
  97. paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  98. paste.recursive.script_name: ''
  99. paste.throw_errors: True
  100. wsgi process: 'Multithreaded'
  101. ------------------------------------------------------------
  102.  
  103.  
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