I upgrade Galaxy to changeset 2531e085f262 and attempt to install freebayes
from the admin panel.

It installed the freebaye xml tool and appears in the tool panel but both
dependencies did not install (freebayes itself and samtools)
When I attempt to install either of them from the  "Tool shed repository
'freebayes' tool dependencies" page , both produces the following error in
the web log:

Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no
attribute 'endswith'
URL:
http://galaxy.badd.ca/admin_toolshed/manage_tool_dependencies?sort=-create_time&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=install&id=33b43b4e7093c91f&;
File
'/opt/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
  app_iter = self.application(environ, start_response)
File '/opt/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
  return self.application(environ, start_response)
File
'/opt/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
  return self.application(environ, start_response)
File '/opt/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 160
in __call__
  body = method( trans, **kwargs )
File '/opt/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line
184 in decorator
  return func( self, trans, *args, **kwargs )
File
'/opt/galaxy/galaxy_dist/lib/galaxy/web/controllers/admin_toolshed.py',
line 902 in manage_tool_dependencies
  self.initiate_tool_dependency_installation( trans,
tool_dependencies_for_installation )
File '/opt/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line
184 in decorator
  return func( self, trans, *args, **kwargs )
File
'/opt/galaxy/galaxy_dist/lib/galaxy/web/controllers/admin_toolshed.py',
line 533 in initiate_tool_dependency_installation
  tool_dependencies=tool_dependencies )
File '/opt/galaxy/galaxy_dist/lib/galaxy/util/shed_util.py', line 1352 in
handle_tool_dependencies
  tool_dependency = install_package( app, elem, tool_shed_repository,
tool_dependencies=tool_dependencies )
File
'/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/tool_dependencies/install_util.py',
line 52 in install_package
  install_dir = get_tool_dependency_install_dir( app, tool_shed_repository,
package_name, package_version )
File
'/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/tool_dependencies/install_util.py',
line 42 in get_tool_dependency_install_dir
  repository.installed_changeset_revision ) )
File '/usr/lib64/python2.6/posixpath.py', line 67 in join
  elif path == '' or path.endswith('/'):
AttributeError: 'NoneType' object has no attribute 'endswith'


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
  HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=0.7,*;q=0.3'
  HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
  HTTP_ACCEPT_LANGUAGE: 'en-GB,en-US;q=0.8,en;q=0.6'
  HTTP_CONNECTION: 'Keep-Alive'
  HTTP_COOKIE:
'galaxysession=c6ca0ddb55be603a1f81117bcdba38660416eeac1cee9b82eec853e080ab1083adff6bfb3578df08'
  HTTP_HOST: 'galaxy.badd.ca'
  HTTP_REFERER: '
http://galaxy.badd.ca/admin_toolshed/manage_tool_dependencies?sort=-create_time&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=uninstall&id=33b43b4e7093c91f&;
'
  HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.1
(KHTML, like Gecko) Chrome/21.0.1180.81 Safari/537.1'
  HTTP_X_FORWARDED_FOR: '10.66.8.100'
  HTTP_X_FORWARDED_HOST: 'galaxy.badd.ca'
  HTTP_X_FORWARDED_SERVER: 'galaxy.badd.ca'
  ORGINAL_HTTP_HOST: 'localhost:8081'
  ORGINAL_REMOTE_ADDR: '127.0.0.1'
  PATH_INFO: '/admin_toolshed/manage_tool_dependencies'
  QUERY_STRING:
'sort=-create_time&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=install&id=33b43b4e7093c91f&'
  REMOTE_ADDR: '10.66.8.100'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '127.0.0.1'
  SERVER_PORT: '8081'
  SERVER_PROTOCOL: 'HTTP/1.1'


Configuration
-------------
  __file__: '/opt/galaxy/galaxy_dist/universe_wsgi.ini'
  admin_users: 'philip.ma...@phac-aspc.gc.ca,chantel.urf...@phac-aspc.gc.ca'
  allow_library_path_paste: 'True'
  allow_user_creation: 'True'
  allow_user_dataset_purge: 'True'
  allow_user_impersonation: 'True'
  api_allow_run_as: 'philip.ma...@phac-aspc.gc.ca'
  database_connection: 'mysql://galaxy:fahn9...@snowwhite.badd.ca/galaxy'
  database_engine_option_pool_recycle: '7200'
  database_engine_option_strategy: 'threadlocal'
  debug: 'False'
  default_cluster_job_runner: 'drmaa://-u forensics-galaxy'
  enable_pages: 'True'
  enable_quotas: 'True'
  enable_tracks: 'True'
  environment_setup_file: '/home/forensics-galaxy/env.sh'
  error_email_to: 'philip.ma...@phac-aspc.gc.ca'
  file_path: '/opt/galaxy/data/database/files'
  here: '/opt/galaxy/galaxy_dist'
  job_handlers: 'handler0,handler1,handler2,handler3'
  job_manager: 'manager'
  len_file_path: 'tool-data/shared/ucsc/chrom'
  library_import_dir: 'None'
  new_file_path: '/opt/galaxy/data/database/tmp'
  new_user_dataset_access_role_default_private: 'True'
  nglims_config_file: 'tool-data/nglims.yaml'
  require_login: 'False'
  retry_metadata_internally: 'False'
  set_metadata_externally: 'True'
  start_job_runners: 'drmaa'
  static_cache_time: '360'
  static_dir: '/opt/galaxy/galaxy_dist/static/'
  static_enabled: 'True'
  static_favicon_dir: '/opt/galaxy/galaxy_dist/static/favicon.ico'
  static_images_dir: '/opt/galaxy/galaxy_dist/static/images'
  static_robots_txt: '/opt/galaxy/galaxy_dist/static/robots.txt'
  static_scripts_dir: '/opt/galaxy/galaxy_dist/static/scripts/'
  static_style_dir: '/opt/galaxy/galaxy_dist/static/june_2007_style/blue'
  tool_config_file: 'tool_conf.xml,shed_tool_conf.xml'
  tool_data_path: 'tool-data'
  tool_path: 'tools'
  use_interactive: 'false'
  use_nglims: 'False'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0x80e7910>
  paste.cookies: (<SimpleCookie:
galaxysession='c6ca0ddb55be603a1f81117bcdba38660416eeac1cee9b82eec853e080ab1083adff6bfb3578df08'>,
'galaxysession=c6ca0ddb55be603a1f81117bcdba38660416eeac1cee9b82eec853e080ab1083adff6bfb3578df08')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object
at 0x80c9c90>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
0x1ac37d0>
  paste.parsed_querystring: ([('sort', '-create_time'),
('show_item_checkboxes', 'false'), ('async', 'false'), ('page', '1'),
('webapp', 'galaxy'), ('operation', 'install'), ('id',
'33b43b4e7093c91f')],
'sort=-create_time&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=install&id=33b43b4e7093c91f&')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  webob._parsed_query_vars: (MultiDict([('sort', '-create_time'),
('show_item_checkboxes', 'false'), ('async', 'false'), ('page', '1'),
('webapp', 'galaxy'), ('operation', 'install'), ('id',
'33b43b4e7093c91f')]),
'sort=-create_time&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=install&id=33b43b4e7093c91f&')
  wsgi process: 'Multithreaded'
------------------------------------------------------------


Philip Mabon
Senior Bioinformatician
National Microbiology Laboratory
Public Health Agency of Canada


On Tue, Aug 28, 2012 at 8:11 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:

> Philip,
>
> Is it possible for you to upgrade your Galaxy instance code base to at
> least changeset 2531e085f262 (the human-readable changeset revision is
> 7503)?  I'm not sure what is causing the behavior in your environment, but
> I had to upgrade the tool shed to this rev in order to deal with some
> issues related to setting metadata on repositories in the tool shed, so
> this may have resulted in problems installing the somewhat special-case
> freebayes repository into local Galaxy instances running the older dist
> release.  You can also choose to wait until the next Galaxy release to
> upgrade if you do not need the freebayes tool in your local instance
> immediately.
>
> Sorry for the inconvenience I'm sure this is causing.
>
> Greg Von Kuster
>
>
> On Aug 27, 2012, at 4:18 PM, Philip Mabon wrote:
>
> I already had that entry to the tool_data_table_conf.xml but still getting
> the same error.
>
> After some debugging and print statement, I found that it initially finds
> the correct path to the 'sam_fa_indexes' when reading
> tool_data_table_conf.xml in Galaxy installation directory but re-reads
> another file in the shed_tools dir.
> It's the sample tool_data_table_conf.xml from the freebayes directory.
> ../shed_tools/
> toolshed.g2.bx.psu.edu/repos/devteam/freebayes/213a3d6b579a/freebayes/tool_data_table_conf.xml.sample
> .
>
> Maybe the  tool_data_table_conf.xml.sample is invalid?
>
> Philip Mabon
> Senior Bioinformatician
> National Microbiology Laboratory
> Public Health Agency of Canada
>
>
> On Mon, Aug 27, 2012 at 9:41 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>
>> Hi Phillip,
>>
>> I'm not able to reproduce this behavior, so it's difficult to determine
>> what may be the cause.  I have not seen others in the community encounter
>> this problem, but that may simply be due to the fact that no one is yet
>> installing the freebayes tool from the tool shed.
>>
>> A possible work-aound is to add the following entry into your local
>> tool_data_table_conf.xml file located in your Galaxy installation directory.
>>
>>     <table name="sam_fa_indexes" comment_char="#">
>>         <columns>line_type, value, path</columns>
>>         <file path="tool-data/sam_fa_indices.loc" />
>>     </table>
>>
>> Let us know if this still does not correct the problem.
>>
>> Greg Von Kuster
>>
>> On Aug 27, 2012, at 10:07 AM, Philip Mabon wrote:
>>
>> Any ideas anyone?
>>
>> Philip Mabon
>> Senior Bioinformatician
>> National Microbiology Laboratory
>> Public Health Agency of Canada
>>
>>
>> On Tue, Aug 21, 2012 at 10:34 AM, Philip Mabon <philipma...@gmail.com>wrote:
>>
>>> I just upgrade our galaxy to the latest release :  7487:be81990d148a and
>>> ran the migration tool script for freebayes.
>>>
>>> I received the following error:
>>>
>>> No handlers could be found for logger "galaxy.tools"
>>> /opt/galaxy/galaxy_dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
>>> RuntimeWarning: __builtin__.file size changed, may indicate binary
>>> incompatibility
>>>   from csamtools import *
>>> Repositories will be installed into configured tool_path location
>>>  ../shed_tools
>>> Adding new row (or updating an existing row) for repository 'freebayes'
>>> in the tool_shed_repository table.
>>> Traceback (most recent call last):
>>>   File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
>>>     app = MigrateToolsApplication( sys.argv[ 1 ] )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/migrate/common.py",
>>> line 150, in __init__
>>>     install_dependencies=install_dependencies )
>>>   File
>>> "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py", line 37,
>>> in __init__
>>>     self.install_repository( repository_elem, install_dependencies )
>>>   File
>>> "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py", line
>>> 262, in install_repository
>>>     install_dependencies=install_dependencies )
>>>   File
>>> "/opt/galaxy/galaxy_dist/lib/galaxy/tool_shed/install_manager.py", line
>>> 150, in handle_repository_contents
>>>     repository_tools_tups = get_repository_tools_tups( self.app,
>>> metadata_dict )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/util/shed_util.py", line
>>> 1077, in get_repository_tools_tups
>>>     tool = app.toolbox.load_tool( os.path.abspath( relative_path ),
>>> guid=guid )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 452,
>>> in load_tool
>>>     return ToolClass( config_file, root, self.app, guid=guid )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 790,
>>> in __init__
>>>     self.parse( root, guid=guid )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 961,
>>> in parse
>>>     self.parse_inputs( root )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line
>>> 1045, in parse_inputs
>>>     display, inputs = self.parse_input_page( page, enctypes )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line
>>> 1447, in parse_input_page
>>>     inputs = self.parse_input_elem( input_elem, enctypes )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line
>>> 1514, in parse_input_elem
>>>     case.inputs = self.parse_input_elem( case_elem, enctypes, context )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line
>>> 1470, in parse_input_elem
>>>     group.inputs = self.parse_input_elem( elem, enctypes, context )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line
>>> 1540, in parse_input_elem
>>>     param = self.parse_param_elem( elem, enctypes, context )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line
>>> 1552, in parse_param_elem
>>>     param = ToolParameter.build( self, input_elem )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py",
>>> line 176, in build
>>>     return parameter_types[param_type]( tool, param )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py",
>>> line 1361, in __init__
>>>     ToolParameter.__init__( self, tool, elem )
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py",
>>> line 43, in __init__
>>>     self.validators.append( validation.Validator.from_element( self,
>>> elem ) )
>>>   File
>>> "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/validation.py", line
>>> 23, in from_element
>>>     return validator_types[type].from_element( param, elem )
>>>   File
>>> "/opt/galaxy/galaxy_dist/lib/galaxy/tools/parameters/validation.py", line
>>> 279, in from_element
>>>     tool_data_table = param.tool.app.tool_data_tables[ table_name ]
>>>   File "/opt/galaxy/galaxy_dist/lib/galaxy/tools/data/__init__.py", line
>>> 25, in __getitem__
>>>     return self.data_tables.__getitem__( key )
>>> KeyError: 'sam_fa_indexes'
>>>
>>>
>>> What happen is that the freebayes itself installs correctly into
>>> the shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/* but the
>>> dependency on samtools 1.1.8 fails.
>>>
>>> The value 'sam_fa_indexes' is present in the tool_data_table_conf.xml
>>>  and I know it works since all my samtools are functional.
>>>
>>> The status column for the freebayes entry in the database is 'Cloning'.
>>>
>>> I get the same error if I try to install freebayes thru the web front
>>> end. ( Had to delete the row in the db and remove the freebayes install
>>> directory)
>>>
>>> Any ideas Greg?
>>>
>>> Thanks!
>>>
>>> Philip Mabon (Takadonet)
>>> Senior Bioinformatician
>>> National Microbiology Laboratory
>>> Public Health Agency of Canada
>>
>>
>> ___________________________________________________________
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>>
>>
>>
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