Re: [galaxy-dev] How to restart the Galaxy process
Hi, try that in your galaxy directory: GALAXY_RUN_ALL=1 sh run.sh --stop-daemon GALAXY_RUN_ALL=1 sh run.sh --daemon Cheers, Bjoern Hello, I modified the Galaxy configuration file and would like to stop and re-start the Galaxy process. Can you tell me how to do that? Thank you. ___ 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ 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/
[galaxy-dev] Running apache as galaxy
Dear all, I had problems configuring apache, which were solved by running apache as user galaxy. Is this an security issue? The server will only be use for galaxy. Cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/
[galaxy-dev] Deleted jobs on the cloud keep running
Dear list, When running Galaxy/Cloudman on Amazon (on Ubuntu 12.04), I run into the following: - I start a job with parallelism in the tool.xml file. - Since I have use_tasked_jobs=True in universe_wsgi.ini, the job is split and divided over the instances on EC2 - I change my mind, and click on the delete button in the Galaxy UI. This removes the job from the UI. - I log in to an instance running my job, and see that it is still running (both its wrapper and the tool program). It keeps running, keeping my instances busy. - When tasks of this job finish (I assume), it is reported to galaxy, and my logfile says things like: galaxy.jobs DEBUG 2012-08-29 12:42:08,239 task 319 for job 25 ended galaxy.jobs DEBUG 2012-08-29 12:42:08,265 The tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2012-08-29 12:42:08,282 task 319 ended So I wonder if the default behaviour when deleting jobs in the UI is that they keep running but hidden, or is there something wrong in my config? Is there a way to change this with a setting? cheers, jorrit boekel ___ 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
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_timeshow_item_checkboxes=falseasync=falsepage=1webapp=galaxyoperation=installid=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_timeshow_item_checkboxes=falseasync=falsepage=1webapp=galaxyoperation=uninstallid=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_timeshow_item_checkboxes=falseasync=falsepage=1webapp=galaxyoperation=installid=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:
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 - type 'exceptions.AttributeError': 'NoneType' object has no
attribute 'endswith'
URL:
http://galaxy.badd.ca/admin_toolshed/manage_tool_dependencies?sort=-create_timeshow_item_checkboxes=falseasync=falsepage=1webapp=galaxyoperation=installid=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_timeshow_item_checkboxes=falseasync=falsepage=1webapp=galaxyoperation=uninstallid=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_timeshow_item_checkboxes=falseasync=falsepage=1webapp=galaxyoperation=installid=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'
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 g...@bx.psu.edu 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 - type 'exceptions.AttributeError': 'NoneType' object has no
attribute 'endswith'
URL:
http://galaxy.badd.ca/admin_toolshed/manage_tool_dependencies?sort=-create_timeshow_item_checkboxes=falseasync=falsepage=1webapp=galaxyoperation=installid=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_timeshow_item_checkboxes=falseasync=falsepage=1webapp=galaxyoperation=uninstallid=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:
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 g...@bx.psu.edu 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 - type 'exceptions.AttributeError': 'NoneType' object has no
attribute 'endswith'
URL:
http://galaxy.badd.ca/admin_toolshed/manage_tool_dependencies?sort=-create_timeshow_item_checkboxes=falseasync=falsepage=1webapp=galaxyoperation=installid=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:
Re: [galaxy-dev] missing slash when installing from toolshed?
Hi, Greg, Thank-you so much for taking the time to answer my question. You appear to be correct; I removed the virtual hosting configuration from apache (I had some redirection configured to automatically forward from port 80 to port 443), and this problem went away. I think I should be able to get things situated from here (I'll try to remember to publish my working config when I get things worked out for for the people that use the mail archive). Again, thank-you for your time and expertise. Dan Sullivan On Tue, Aug 28, 2012 at 5:10 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Dan, The only thing I can think of that is causing this behavior is an apache rewrite rule that is not correctly handling your base URL. That's the only scenario in which I've seen something like this occur, but others in the community may have seen other causes. I'm fairly certain it has something to do with the server configuration (not a Galaxy issue). Greg Von Kuster On Aug 22, 2012, at 3:18 PM, Dan Sullivan wrote: I apologize for spamming this list, the screenshot that I specified as attached was supplied in a hyperlink farther down in the mail (not as an attachment). https://webshare.uchicago.edu/users/dansully/Public/Screen%20Shot%202012-08-21%20at%203.22.27%20PM.png Dan On Aug 22, 2012, at 10:13 AM, Dan Sullivan dansulli...@gmail.com wrote: Hi, Galaxy Developers, I have a question that is very similar to the following thread; http://dev.list.galaxyproject.org/Problem-fetching-updates-to-toolshed-tool-td4353417.html Basically whenever I try to install a tool from the toolshed, it appears that a trailing slash is not appended to the Galaxy URL, which is causing a DNS lookup failure. For example, the URL specified in the attached screenshot should be https://crigalaxy.uchicago.edu/admin_toolshed, however it is appearing as https://crigalaxy.uchicago.eduadmin_toolshed.Does anybody know if there are any known bugs that would cause this behavior? I might venture down the road of modifying lib/galaxy/webapps/community/controllers/repository.py as suggested by the thread above, although I would like to avoid doing this if possible. I am seeing experiencing this behavior on the following version of Galaxy: hg parent changeset: 7400:ec29ce8e27a1 In addition to this, I feel that its worthwhile to mention that I am using the apache proxy balancer with web scaling, however based on what I have seen and tested, I do not believe this (apache) to be the root cause of my problem. The URL below is a screenshot of the network debug I am seeing from the firebug extension in firefox. https://webshare.uchicago.edu/users/dansully/Public/Screen%20Shot%202012-08-21%20at%203.22.27%20PM.png If somebody has seen this, or could offer a suggestion to bring this issue to resolve, I would definitely be interested in your strategy. Thank-you so much for your help and for your time. Dan Sullivan 312-607-3702 ___ 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/
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 -iSPACE.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
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 gor...@cshl.edu 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 -iSPACE.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] upload files by cluster with pbs-python returns empty files
On Jul 16, 2012, at 6:14 AM, Geert Vandeweyer wrote: Hi, We have set up a local instance of galaxy-dist, using pbs-python to communicate with our HPC. Everything is working great, except for the upload functionality. When I assign the upload1 to local:/// , uploading of small files through the web-site works, and upload of large files by ftp works as well. When I let upload1 to be handled by the default_cluster_job_runner ( = pbs:///), I get empty data sets. Galaxy does not report any errors however and the data state is ok. Has anybody seen this issue and solved it? Using the local:/// job handler causes a massive performance hit on the galaxy process. Best regards, Geert Vandeweyer Hi Geert, Sorry for the delayed response. If you're still having this issue, if you view the empty dataset, can you see the data it's supposed to contain? i.e. does the underlying output file for the upload tool actually contain the data, or is it really empty on disk? --nate ___ 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/
Re: [galaxy-dev] patch contribution (was Re: So I think I fixed a bug.)
Great, I am glad it was useful. Renaming the repository isn't needed, especially if you just have one pull request open at a time. But there have been times I have had maybe 4 or 5 open pull requests at once, so then it helps to keep track of which repository maps to which feature or bug fix. If I logged into bitbucket and saw galaxy-central-1,galaxy-central-2, galaxy-central-3, that wouldn't be as informative. -John On Tue, Aug 28, 2012 at 8:11 PM, Clare Sloggett s...@unimelb.edu.au wrote: Hi John, Thank you, this is really useful! I don't understand the purpose of renaming the repository to galaxy-central-new-feature - what does this achieve? I'm pretty new to mercurial and more familiar with git, so that could be why I'm confused. Thanks, Clare On 24 August 2012 00:07, John Chilton chil...@msi.umn.edu wrote: I don't know that difficult is the right word, I would call the process heavy handed and time consuming, especially relative to similar git workflows. I have heard the Galaxy developers say on multiple occasions the prefer pull requests coming using a dedicated clone though and this makes a lot of sense because branches stick around forever in mercurial. So I now use dedicated repositories for each of my pull requests. I am still trying to optimize my workflow, but here is a high level overview of my current process. We have a local version of Galaxy (lets call it msi-galaxy), if we want to push changes back I generally create a dedicated clone of galaxy-central on bitbucket for this change (say galaxy-central-feature1) and then export the desired revision/revisions as a patch from our local branch and import it in my feature clone. % cd msi-galaxy % hg export -r rev1 -r rev2 /tmp/feature1.patch % cd .. % hg clone ssh://h...@bitbucket.org/jmchilton/galaxy-central-feature1 % cd galaxy-central-feature1 % hg import /tmp/feature1.patch % hg push Create pull request. Other tricks I have learned: Use ssh keys for bitbucket interactions instead of https, it seems considerably faster. You can add --no-commit to the import and then manually commit. This can let you map multiple changesets from your local branch to the feature clone (a poor man's rebasing I guess). The longest part of the process is the original clone down of the feature clones. So I have just started reusing old clones for this. - Rename galaxy-central-old-feature to galaxy-central-new-feature on bitbucket. - % cd galaxy-central-old-feature - % hg pull ssh://h...@bitbucket.org/galaxy/galaxy-central # catch up with galaxy-central - Make changes - % hg push ssh://h...@bitbucket.org/jmchilton/galaxy-central-new-feature - Create pull request. The downside of this cheat is that previously accept pull requests now have source repository names associated with them in bitbucket, like this https://bitbucket.org/galaxy/galaxy-central/pull-request/44/allow-usage-of-directory-of-configuration. -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 On Thu, Aug 23, 2012 at 8:29 AM, Langhorst, Brad langho...@neb.com wrote: Maybe I'm just doing it wrong… but I find it unusually difficult to put together a coherent pull request without doing a dedicated repo clone. maybe somebody who knows a good way to submit pull requests could populate this wiki page? http://wiki.g2.bx.psu.edu/Develop/Mercurial brad On Aug 23, 2012, at 8:55 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote: For a simple patch like yours, just pasting and sending your diff to the list works well: %hg diff ... For bigger patches/enhancements, a bitbucket fork + pull request is highly encouraged. Best, J. On Aug 23, 2012, at 4:47 AM, James wrote: Hi All, Today I found a bug relating to the file permissions in composite datatypes. When the extrafiles directory was created and the server was running through apache, the permission did not allow a galaxy user to download by following the HTML link. Found it was related to meta data files not using the os.chmod function to set the permissions of the user data in upload.py. Added that line of code and it works and the file permissions match that of other files in the database. Somehelp with submitting a patch would be welcome ( although one line patch it would be helpful to me.) Cheers James Boocock ___ 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:
[galaxy-dev] Issues with database / metadata after upgrade
Hi Team, I had performed an upgrade of my Galaxy server and had experienced an issue with some of the database / metadata files have been corrupted. I have found instances where the dataset exists, but cannot be detected or read by galaxy when attempting to analysis data from a history. In some cases I have been able to locate another copy and replace the damaged file. What might have been the cause and is there a way to resolve it? Is this a possible Postgres issue or since the metadata is contained in the /database/files/ directory an artifact of the upgrade? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ 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] xsendfile permissions
On Jul 17, 2012, at 3:16 PM, Julian Pradinuk wrote: Hi all, I'm wondering if someone who has downloads working through apache (using xsendfile) has encountered this error when downloading HTML files: (13)Permission denied: xsendfile: cannot open file: /galaxy_data/production/tmp/tmpN0ydYt/library_download.zip The output from ls -lZ /galaxy_data/production/tmp is: ... drwx--. galaxy galaxy unconfined_u:object_r:httpd_sys_content_t:s0 tmpN0ydYt ... The output from ls-lZ /galaxy_data/production/tmp/tmpN0ydYt/ is: -rw-rw-r--. galaxy galaxy unconfined_u:object_r:httpd_sys_content_t:s0 library_download.zip Hi Julian, This should be fixed in 7588:068a043f6bb1, which will be in our next stable release. You'll need to make sure that your Galaxy server process starts under a umask(2) that will give group and/or other permissions. If you allow group-only access, your Galaxy user will need to start with a group that your Apache server is a member of. --nate It's not a SElinux issue (if I sudo setenforce 0, the problem persists).. It seems it's a regular permissions issue (user apache is running httpd and does not permission to enter the tmpN0ydYt). Since galaxy creates these files with these permissions I don't know how to fix this issue. I'm also wondering why the HTML datasets are in the tmp folder not the files folder? Here's my apache config: VirtualHost *:80 ServerName RewriteEngine on #RewriteOptions Inherit #RewriteLog /etc/httpd/logs/rewrite_log #RewriteLogLevel 5 RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /usr/local/galaxy/production/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /usr/local/galaxy/production/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /usr/local/galaxy/production/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /usr/local/galaxy/production/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /usr/local/galaxy/production/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] Location /galaxy order allow,deny allow from all # Compress all uncompressed content SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary # Send files through Apache XSendFile on XSendFilePath /galaxy_data /Location Location /galaxy/static # Allow browsers to cache everything from /static for 6 hours ExpiresActive On ExpiresDefault access plus 6 hours /Location /VirtualHost Is there something wrong with it? Or have I missed something in universe.wsgi? Cheers, Julian ___ 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/
Re: [galaxy-dev] Tool test question
On Jul 18, 2012, at 5:02 PM, christopher fletez-brant wrote: Hi Nate, The test XML is: tests test param name=input value=nullseq_test.bed ftype=bed / param name=fold value=1 / param name=gc_err value=0.02 / param name=rpt_err value=0'02 / param name=rseed value=1 / param name=indices_path value=hg19 / output name=output file=nullseq_output.bed / /test /tests And the XML for the problematic parameter, indices_path, is: param name=indices_path type=select label=Available Datasets options from_file=nullseq_indices.loc column name=dbkey index=0/ column name=value index=0/ column name=name index=1/ column name=path index=2/ !--filter type=data_meta ref=input key=dbkey column=0 /-- /options /param Hi, Sorry I didn't get back to you. If you set your upload's dbkey to hg19, e.g.: param name=input value=nullseq_test.bed ftype=bed dbkey=hg19 / I believe it'll fix the issue. --nate Thanks for the reply! On Wed, Jul 18, 2012 at 3:55 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 18, 2012, at 2:55 PM, christopher fletez-brant wrote: Hi, just wondering if anyone has any insight into this issue, as it is driving me crazy, especially given that the correct list control element is selected (hg19). From the output you sent, it doesn't look like your tool is actually running, just the upload. What does your test XML look like? --nate On Sat, Jul 14, 2012 at 8:54 PM, christopher fletez-brant cafletezbr...@gmail.com wrote: Hi Nate, Thanks for the reply. Error messages are output at the bottom of the message. Setup is that the tool has a number of inputs, one of which is actually a directory containing reference files. We pass the directory by allowing users to select from a menu the genome whose information is held in that directory; this is done by means of a *.loc file, whose value in the tool config is 'indices_path' below. Run from the Galaxy server, this tool works perfectly. However, I think that perhaps it cannot find the directory for some reason? I just note that diff reports the values listed as missing, but no '+' values indicating what is in their place. Any advice would be appreciated. Thank you, Kipper alaxy.tools.actions.upload_common INFO 2012-07-14 20:39:41,302 tool upload1 created job id 1 galaxy.jobs.manager DEBUG 2012-07-14 20:39:47,663 (1) Job assigned to handler 'main' galaxy.jobs DEBUG 2012-07-14 20:39:52,828 (1) Working directory for job is: /home/fake/galaxy-dist/database/job_working_directory/000/1 galaxy.jobs.handler DEBUG 2012-07-14 20:39:52,829 dispatching job 1 to local runner galaxy.jobs.handler INFO 2012-07-14 20:39:53,008 (1) Job dispatched galaxy.jobs.runners.local DEBUG 2012-07-14 20:39:53,255 executing: python /home/fake/galaxy-dist/tools/data_source/upload.py /home/fake/galaxy-dist /tmp/tmpeEp5KR/database/tmp/tmpfYngg0 /tmp/tmpeEp5KR/database/tmp/tmpMKsPIL 1:/home/fake/galaxy-dist/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpeEp5KR/database/files/000/dataset_1.dat galaxy.jobs.runners.local DEBUG 2012-07-14 20:39:54,480 execution finished: python /home/fake/galaxy-dist/tools/data_source/upload.py /home/fake/galaxy-dist /tmp/tmpeEp5KR/database/tmp/tmpfYngg0 /tmp/tmpeEp5KR/database/tmp/tmpMKsPIL 1:/home/fake/galaxy-dist/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpeEp5KR/database/files/000/dataset_1.dat galaxy.jobs DEBUG 2012-07-14 20:39:54,759 job 1 ended base.twilltestcase INFO 2012-07-14 20:39:55,782 ## files diff on /home/fake/galaxy-dist/test-data/nullseq_output.bed and /tmp/tmpeEp5KR/database/tmp/tmpuT588_nullseq_output.bed lines_diff=0, found diff = 200 -- begin tool stdout --- --- end tool stdout -- begin tool stderr --- --- end tool stderr FAIL == FAIL: test_tool_00 (functional.test_toolbox.TestForTool_kmersvm_nullseq) Generate Null Sequence ( kmersvm_nullseq ) Test-1 -- Traceback (most recent call last): File /home/fake/galaxy-dist/test/functional/test_toolbox.py, line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /home/fake/galaxy-dist/test/functional/test_toolbox.py, line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File /home/fake/galaxy-dist/test/base/twilltestcase.py, line 733, in verify_dataset_correctness raise
[galaxy-dev] using data_ref to refer to column names?
Hi, I have some code that makes a plot and creates a legend from a given column name in the user's input data, which may have arbitrary column names. I'd like to create a dropdown list that has all the column names in it, but I don't know the names beforehand; I won't know them until the user uploads their data file. So all I can do is have a freeform text box where I ask the user to type a column name, which seems error-prone and ugly. I notice that the XY plotting tool has something sort of like this, where it can tell how many columns are in your dataset and lets you choose them, but it calls the columns c1, c2, etc. My datasets have a header line with column names and I want to show the actual column name, not reference them by column number. Is this possible? Is there a solution to this? I have a number of use cases like this, so it would be great if there was. Thanks, Dan ___ 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/
[galaxy-dev] Blastxml error on Galaxy Cloudman
Hello, I recently updated my instance of Galaxy Cloudman (using Amazon AWS) and I have since not been able to run any jobs. I get the following error: WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no attribute 'BlastXml' Any help would greatly be appreciated. Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 ___ 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] Blastxml error on Galaxy Cloudman
Hi The BLAST+ tools and the definition of the blastxml format were moved to the tool shed. You should have seen a migration message during the update... If you are not using these tools, perhaps you have a legacy reference to the blastxml file which should be removed? If you are using BLAST+ they and the blastxml format need to be installed from the ToolShed, Peter On Wednesday, August 29, 2012, Mohammad Heydarian wrote: Hello, I recently updated my instance of Galaxy Cloudman (using Amazon AWS) and I have since not been able to run any jobs. I get the following error: WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no attribute 'BlastXml' Any help would greatly be appreciated. Cheers, Mo Heydarian ___ 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] get wsgi headers
On Aug 24, 2012, at 9:48 AM, Mutlu Dogruel wrote: Hi folk, Do you know any method for reading (the extended) WSGI HTTP headers from a custom tool? If I put some debugging lines in $galaxy/lib/galaxy/web/framework/middleware/xforwardedhost.py, I can read the HTTP headers I want. But I need to access them under tools/my_script.py. Is there a way to reach the webapps http headers from there? Hi Mutlu, Do you mean the headers at the time of tool execution? Running tools (jobs) is intentionally decoupled from the state of the front end. However, you could modify the tool submission to store the header as a tool parameter and pass it in the command template. --nate Thanks. Mutlu ___ 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/
Re: [galaxy-dev] Modules
galaxy already has tool-dependencies which can be used. for example, velvet's tool XML would include: requirements requirement type=packagevelvet/requirement /requirements the above will use the default version; or to specify a specific version: requirements requirement type=package version=1.2.07velvet/requirement /requirements in your tool-dependencies dir (as defined in universe_wsgi.ini): mkdir velvet cd velvet mkdir 1.2.07 mkdir DEFAULT ln -s DEFAULT/ default echo module load velvet/1.2.07 1.2.07/env.sh echo module load velvet DEFAULT/env.sh notes: - type must be package - default must be a symlink - we had to add -S /bin/bash -shell y to DRMAA native spec to get the bash module function we use to work; may not be an issue with you. Ed On Tue, Aug 28, 2012 at 7:28 AM, Fabien Mareuil fabien.mare...@pasteur.frwrote: Dear Colleagues, Many teams use module, a user interface for the Modules package. The Modules package enable to manage easily several versions of a program with a dynamic modification of the user's environment via modulefiles. I would like to know if it is planned to integrate the ability to load modules via galaxy? For example, we could imagine a configuration file that would link the name and version of a tool with the module name and allowing to load the module before running the tool locally or on a cluster. Thank you for your answer, Best regards, Fabien Mareuil ___ 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/
[galaxy-dev] September 2012 Galaxy Update
Hello all, The September 2012 Galaxy Update is now availablehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09. *Highlights:* - 41 new papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#New_Papers(a new monthly high) - 3 new public Galaxy Servershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#New_Public_Servers - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#Who.27s_Hiringat four different institutions - Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#Upcoming_Events_and_Deadlines - Swiss Galaxy Day is October 3!http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#Swiss_Galaxy_Day - New Galaxy-France mailing listhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#New_Galaxy-France_Mailing_List - Tool Shed Contributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#Tool_Shed_Contributions - Other News http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#Other_News If you have anything you would like to see in the October *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates *, please let me know. Thanks, Dave Clements -- http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09 http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] Blastxml error on Galaxy Cloudman
Hi Mohammad,
Don't forget to CC the mailing list ;)
It sounds like something has gone wrong with the update...
Peter
On Wednesday, August 29, 2012, Mohammad Heydarian wrote:
Hi Peter,
Thanks for your response.
I am not using any of the Blast tools, I have only tried using the filter
and sort and text manipulation tools and gotten this error.
Could this be fixed by re-updating my instance of Galaxy Cloudman? Or some
similar fix? I am not able to install tools to my instance of Galaxy
Cloudman, the error I get is:
The *tool_config_file* setting in *universe_wsgi.ini* must include at
least one shed tool configuration file name with a *toolbox* tag that
includes a *tool_path* attribute value which is a directory relative to
the Galaxy installation directory in order to automatically install tools
from a Galaxy tool shed (e.g., the file name *shed_tool_conf.xml* whose *
toolbox* tag is *toolbox tool_path=../shed_tools*).
Cheers,
Mo Heydarian
PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe Street
414 Hunterian
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On Wed, Aug 29, 2012 at 3:24 PM, Peter Cock
p.j.a.c...@googlemail.comjavascript:_e({}, 'cvml',
'p.j.a.c...@googlemail.com');
wrote:
Hi
The BLAST+ tools and the definition of the blastxml format were moved to
the tool shed. You should have seen a migration message during the update...
If you are not using these tools, perhaps you have a legacy reference to
the blastxml file which should be removed?
If you are using BLAST+ they and the blastxml format need to be installed
from the ToolShed,
Peter
On Wednesday, August 29, 2012, Mohammad Heydarian wrote:
Hello,
I recently updated my instance of Galaxy Cloudman (using Amazon AWS) and
I have since not been able to run any jobs. I get the following error:
WARNING:galaxy.datatypes.registry:Error loading datatype with extension
'blastxml': 'module' object has no attribute 'BlastXml'
WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype
'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no
attribute 'BlastXml'
Any help would greatly be appreciated.
Cheers,
Mo Heydarian
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[galaxy-dev] LSF DRMAA/FedStage config-make errors
Hello all, I am trying to get a Galaxy server configured to submit jobs to an LSF cluster running version 7 update 2, generally CentOS/Redhat 5 systems. I have the Galaxy host as a client in LSF, but when I tried to configure/make/install the FedStage drmaa code, it errors out in the make stage (see stdout below). Don't know what to fix, if it's possible. If anyone has experience configuring/troubleshooting this code to get Galaxy conversant with LSF, I'd appreciate any feedback. Thanks! Regards, Doug _ util.c: In function 'lsfdrmaa_map_lsberrno': util.c:730: error: 'LSBE_ADRSV_ID_UNIQUE' undeclared (first use in this function) util.c:730: error: (Each undeclared identifier is reported only once util.c:730: error: for each function it appears in.) util.c:731: error: 'LSBE_BAD_RSVNAME' undeclared (first use in this function) util.c:732: error: 'LSBE_BAD_CHKPNTDIR' undeclared (first use in this function) util.c:734: error: 'LSBE_JOB_REQUEUE_BADEXCLUDE' undeclared (first use in this function) util.c:737: error: 'LSBE_ADVRSV_ACTIVESTART' undeclared (first use in this function) util.c:739: error: 'LSBE_ADRSV_ID_USED' undeclared (first use in this function) util.c:740: error: 'LSBE_ADRSV_PREVDISABLED' undeclared (first use in this function) util.c:742: error: 'LSBE_ADRSV_DISABLECURR' undeclared (first use in this function) util.c:744: error: 'LSBE_ADRSV_NOT_RSV_HOST' undeclared (first use in this function) util.c:749: error: 'LSBE_ADRSV_MOD_REMOTE' undeclared (first use in this function) util.c:751: error: 'LSBE_JOB_RUSAGE_EXCEED_LIMIT' undeclared (first use in this function) util.c:752: error: 'LSBE_APP_RUSAGE_EXCEED_LIMIT' undeclared (first use in this function) util.c:755: error: 'LSBE_ADRSV_DISABLE_DATE' undeclared (first use in this function) util.c:759: error: 'LSBE_ADRSV_DETACH_MIX' undeclared (first use in this function) util.c:761: error: 'LSBE_ADRSV_DETACH_ACTIVE' undeclared (first use in this function) util.c:765: error: 'LSBE_MISSING_START_END_TIME' undeclared (first use in this function) make[3]: *** [libdrmaa_la-util.lo] Error 1 make[3]: Leaving directory `/root/installers/lsf_drmaa-1.0.4/lsf_drmaa' make[2]: *** [all] Error 2 make[2]: Leaving directory `/root/installers/lsf_drmaa-1.0.4/lsf_drmaa' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/root/installers/lsf_drmaa-1.0.4' (Same output with version 1.0.3.) This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as E-Contract Intended, this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html ___ 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/
