Re: [galaxy-dev] Error with tool migration
Kerry, Greg's fix in 11800:a53f2f700699 has been applied to the stable branch as 11804:a9a0ac9c1afa, and the galaxy-dist repository has been updated to that changeset. --Dave B. On 12/18/2013 07:14 PM, Kerry Deutsch wrote: No, we're pulling galaxy-dist. Thanks for the quick reply, Kerry On Wed, Dec 18, 2013 at 4:07 PM, Greg Von Kuster g...@bx.psu.edu mailto:g...@bx.psu.edu wrote: Hello Kerry, I've committed a fix for this in 11800:a53f2f700699 to the galaxy-central branch. Is that the branch you're pulling? Thanks for reporting this. Greg Von Kuster On Dec 18, 2013, at 5:48 PM, Kerry Deutsch kerry.deut...@systemsbiology.org mailto:kerry.deut...@systemsbiology.org wrote: Hello - I pulled down the latest changes today (it was long overdue), and am running into the following error when I run the tool migration: sh ./scripts/migrate_tools/0008_tools.sh install_dependencies No handlers could be found for logger galaxy.tools.data Repositories will be installed into configured tool_path location ../shed_tools [localhost] local: rm -rf ./database/tmp/tmp-toolshed-mtdWuQjBx Skipping installation of tool dependency samtools version 0.1.18 since it is installed in /users/galaxy/galaxy_deps/bin/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d Traceback (most recent call last): File ./scripts/migrate_tools/migrate_tools.py, line 21, in module app = MigrateToolsApplication( sys.argv[ 1 ] ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py, line 83, in __init__ install_dependencies=install_dependencies ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 121, in __init__ is_repository_dependency=is_repository_dependency ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 509, in install_repository is_repository_dependency=is_repository_dependency ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 351, in handle_repository_contents guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 259, in get_guid full_path = str( os.path.abspath( os.path.join( root, name ) ) ) UnboundLocalError: local variable 'name' referenced before assignment Ideas? Thanks much! Kerry ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Error with tool migration
Hello - I pulled down the latest changes today (it was long overdue), and am running into the following error when I run the tool migration: sh ./scripts/migrate_tools/0008_tools.sh install_dependencies No handlers could be found for logger galaxy.tools.data Repositories will be installed into configured tool_path location ../shed_tools [localhost] local: rm -rf ./database/tmp/tmp-toolshed-mtdWuQjBx Skipping installation of tool dependency samtools version 0.1.18 since it is installed in /users/galaxy/galaxy_deps/bin/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d Traceback (most recent call last): File ./scripts/migrate_tools/migrate_tools.py, line 21, in module app = MigrateToolsApplication( sys.argv[ 1 ] ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py, line 83, in __init__ install_dependencies=install_dependencies ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 121, in __init__ is_repository_dependency=is_repository_dependency ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 509, in install_repository is_repository_dependency=is_repository_dependency ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 351, in handle_repository_contents guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 259, in get_guid full_path = str( os.path.abspath( os.path.join( root, name ) ) ) UnboundLocalError: local variable 'name' referenced before assignment Ideas? Thanks much! Kerry ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error with tool migration
Hello Kerry, I've committed a fix for this in 11800:a53f2f700699 to the galaxy-central branch. Is that the branch you're pulling? Thanks for reporting this. Greg Von Kuster On Dec 18, 2013, at 5:48 PM, Kerry Deutsch kerry.deut...@systemsbiology.org wrote: Hello - I pulled down the latest changes today (it was long overdue), and am running into the following error when I run the tool migration: sh ./scripts/migrate_tools/0008_tools.sh install_dependencies No handlers could be found for logger galaxy.tools.data Repositories will be installed into configured tool_path location ../shed_tools [localhost] local: rm -rf ./database/tmp/tmp-toolshed-mtdWuQjBx Skipping installation of tool dependency samtools version 0.1.18 since it is installed in /users/galaxy/galaxy_deps/bin/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d Traceback (most recent call last): File ./scripts/migrate_tools/migrate_tools.py, line 21, in module app = MigrateToolsApplication( sys.argv[ 1 ] ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py, line 83, in __init__ install_dependencies=install_dependencies ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 121, in __init__ is_repository_dependency=is_repository_dependency ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 509, in install_repository is_repository_dependency=is_repository_dependency ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 351, in handle_repository_contents guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 259, in get_guid full_path = str( os.path.abspath( os.path.join( root, name ) ) ) UnboundLocalError: local variable 'name' referenced before assignment Ideas? Thanks much! Kerry ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error with tool migration
No, we're pulling galaxy-dist. Thanks for the quick reply, Kerry On Wed, Dec 18, 2013 at 4:07 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Kerry, I've committed a fix for this in 11800:a53f2f700699 to the galaxy-central branch. Is that the branch you're pulling? Thanks for reporting this. Greg Von Kuster On Dec 18, 2013, at 5:48 PM, Kerry Deutsch kerry.deut...@systemsbiology.org wrote: Hello - I pulled down the latest changes today (it was long overdue), and am running into the following error when I run the tool migration: sh ./scripts/migrate_tools/0008_tools.sh install_dependencies No handlers could be found for logger galaxy.tools.data Repositories will be installed into configured tool_path location ../shed_tools [localhost] local: rm -rf ./database/tmp/tmp-toolshed-mtdWuQjBx Skipping installation of tool dependency samtools version 0.1.18 since it is installed in /users/galaxy/galaxy_deps/bin/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d Traceback (most recent call last): File ./scripts/migrate_tools/migrate_tools.py, line 21, in module app = MigrateToolsApplication( sys.argv[ 1 ] ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py, line 83, in __init__ install_dependencies=install_dependencies ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 121, in __init__ is_repository_dependency=is_repository_dependency ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 509, in install_repository is_repository_dependency=is_repository_dependency ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 351, in handle_repository_contents guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 259, in get_guid full_path = str( os.path.abspath( os.path.join( root, name ) ) ) UnboundLocalError: local variable 'name' referenced before assignment Ideas? Thanks much! Kerry ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
