Hi Philip,

What do you have for the following configuration setting in the [app:main] 
section of your universe_wsgi.ini file?  The config setting for 
tool_dependency_dir should be a valid subdirectory that is writable by the user 
that starts your Galaxy server.

# Location for installing tool dependencies
tool_dependency_dir = ../tool_dependencies

Greg Von Kuster


On Aug 29, 2012, at 9:34 AM, Philip Mabon wrote:

> 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
>>> 
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> 
>>>  http://lists.bx.psu.edu/
>> 
>> 
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> 
>>  http://lists.bx.psu.edu/
> 
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to