Re: [galaxy-dev] Cannot install freebayes with migration script
That's pretty much what I had to do. Thanks for the full explanation so others will know! Philip Mabon Senior Bioinformatician National Microbiology Laboratory Public Health Agency of Canada On Wed, Aug 29, 2012 at 10:31 AM, Assaf Gordon wrote: > Hello Philip, > > Philip Mabon wrote, On 08/29/2012 10:08 AM: > > Looks like I forgot to reset that value. So making progress... I can > install freebayes successfully (the front end timeout but it worked) > > > > However, samtools fails with the following message in web worker log: > > > > [localhost] local: sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile > > Warning: local() encountered an error (return code 2) while executing > 'sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile' > > > > Front end error: "sed: can't read .bak: No such file or directory" > > > > So for some reason the sed did not work... > > > > I haven't followed the full thread, but the direct reason for this error > (with 'sed') is that the command-line uses a Mac/BSD syntax which is not > standard and not compatible with the most common linux version of sed. > > The parameter "-i" instructs sed to work in-place, and create a backup > with with the given extension. > Mac/BSD sed accepts "-i.bak" and "-i.bak" (without space), but the > GNU sed does not accept a space, and so assumes that ".bak" is the input > file name you want to work on (which obviously doesn't exist, hence the > error "no such file"). > > So the following are identical on Mac: > sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile > sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile > > But with GNU sed, the first one will not work as expected. > > To fix it, simply remove the space after the "-i" parameter (I'm not sure > where the command is - is it part of freebayes or part of the tool-shed). > > Regards, > -gordon > > > ___ 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/
Re: [galaxy-dev] Cannot install freebayes with migration script
Hello Philip, Philip Mabon wrote, On 08/29/2012 10:08 AM: > Looks like I forgot to reset that value. So making progress... I can install > freebayes successfully (the front end timeout but it worked) > > However, samtools fails with the following message in web worker log: > > [localhost] local: sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile > Warning: local() encountered an error (return code 2) while executing 'sed -i > .bak -e 's/-lcurses/-lncurses/g' Makefile' > > Front end error: "sed: can't read .bak: No such file or directory" > > So for some reason the sed did not work... > I haven't followed the full thread, but the direct reason for this error (with 'sed') is that the command-line uses a Mac/BSD syntax which is not standard and not compatible with the most common linux version of sed. The parameter "-i" instructs sed to work in-place, and create a backup with with the given extension. Mac/BSD sed accepts "-i.bak" and "-i.bak" (without space), but the GNU sed does not accept a space, and so assumes that ".bak" is the input file name you want to work on (which obviously doesn't exist, hence the error "no such file"). So the following are identical on Mac: sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile But with GNU sed, the first one will not work as expected. To fix it, simply remove the space after the "-i" parameter (I'm not sure where the command is - is it part of freebayes or part of the tool-shed). Regards, -gordon ___ 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/
Re: [galaxy-dev] Cannot install freebayes with migration script
You should be able to click on the link for the samtools dependency from the
"Installed tool shed repository" page for freebayes. Clicking the link will
allow you to browse the INSTALLATION.LOG on disk and see what caused the
error. Your environment is probably missing some component required to compile
samtools. If you find out what is missing from your environment you'll have to
install it. Then uninstall the samtools dependency using the Galaxy UI and
attempt to install it again.
Greg Von Kuster
On Aug 29, 2012, at 10:08 AM, Philip Mabon wrote:
> Looks like I forgot to reset that value. So making progress... I can install
> freebayes successfully (the front end timeout but it worked)
>
> However, samtools fails with the following message in web worker log:
>
> [localhost] local: sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile
> Warning: local() encountered an error (return code 2) while executing 'sed -i
> .bak -e 's/-lcurses/-lncurses/g' Makefile'
>
> Front end error: "sed: can't read .bak: No such file or directory"
>
> So for some reason the sed did not work...
>
>
> Philip Mabon
> Senior Bioinformatician
> National Microbiology Laboratory
> Public Health Agency of Canada
>
>
> On Wed, Aug 29, 2012 at 8:48 AM, Greg Von Kuster wrote:
> 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 - : '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=c6ca0ddb55be603a1f81117bcdba38660416
Re: [galaxy-dev] Cannot install freebayes with migration script
Looks like I forgot to reset that value. So making progress... I can
install freebayes successfully (the front end timeout but it worked)
However, samtools fails with the following message in web worker log:
[localhost] local: sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile
Warning: local() encountered an error (return code 2) while executing 'sed
-i .bak -e 's/-lcurses/-lncurses/g' Makefile'
Front end error: "sed: can't read .bak: No such file or directory"
So for some reason the sed did not work...
Philip Mabon
Senior Bioinformatician
National Microbiology Laboratory
Public Health Agency of Canada
On Wed, Aug 29, 2012 at 8:48 AM, Greg Von Kuster wrote:
> 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 - : '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&s
Re: [galaxy-dev] Cannot install freebayes with migration script
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 - : '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...@snowwhi
Re: [galaxy-dev] Cannot install freebayes with migration script
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 - : '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/tm
Re: [galaxy-dev] Cannot install freebayes with migration script
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 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. > > > line_type, value, path > > > > 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 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 >> 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 = se
Re: [galaxy-dev] Cannot install freebayes with migration script
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 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. > > > line_type, value, path > > > > 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 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 >> 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_dis
Re: [galaxy-dev] Cannot install freebayes with migration script
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. line_type, value, path 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 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 > 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 d
Re: [galaxy-dev] Cannot install freebayes with migration script
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 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 > 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
