Re: [galaxy-dev] Error installing migrated tool deps
Confirmed working, thanks! -Branden On 5/7/2013 1:25 PM, Dave Bouvier wrote: Branden, Thank you for reporting this issue, I've committed a fix in 9662:6c462a5a566d. You should be able to re-run your tool migration after updating to that revision. --Dave B. On 5/7/13 11:09:31.000, Branden Timm wrote: I recently upgraded to the latest galaxy-central, and was advised on first run that two tools in tool_conf.xml had been removed from the distribution, but could be installed from the tool shed. I ran the script that it generated, however the script fails with the following messages: No handlers could be found for logger galaxy.tools.parameters.dynamic_options /home/GLBRCORG/galaxy/galaxy-central/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 Skipping automatic install of repository ' bowtie_wrappers ' because it has already been installed in location ../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/0c7e4eadfb3c Traceback (most recent call last): File ./scripts/migrate_tools/migrate_tools.py, line 21, in module app = MigrateToolsApplication( sys.argv[ 1 ] ) File /home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/migrate/common.py, line 76, in __init__ install_dependencies=install_dependencies ) File /home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py, line 75, in __init__ self.install_repository( repository_elem, install_dependencies ) File /home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py, line 319, in install_repository install_dependencies=install_dependencies ) File /home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py, line 203, in handle_repository_contents persist=True ) File /home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/util/metadata_util.py, line 594, in generate_metadata_for_changeset_revision tool, valid, error_message = tool_util.load_tool_from_config( app, app.security.encode_id( repository.id ), full_path ) AttributeError: 'MigrateToolsApplication' object has no attribute 'security' Any help would be greatly appreciated. Thanks! -- Branden Timm bt...@energy.wisc.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/ 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 installing migrated tool deps
Branden, Thank you for reporting this issue, I've committed a fix in 9662:6c462a5a566d. You should be able to re-run your tool migration after updating to that revision. --Dave B. On 5/7/13 11:09:31.000, Branden Timm wrote: I recently upgraded to the latest galaxy-central, and was advised on first run that two tools in tool_conf.xml had been removed from the distribution, but could be installed from the tool shed. I ran the script that it generated, however the script fails with the following messages: No handlers could be found for logger galaxy.tools.parameters.dynamic_options /home/GLBRCORG/galaxy/galaxy-central/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 Skipping automatic install of repository ' bowtie_wrappers ' because it has already been installed in location ../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/0c7e4eadfb3c Traceback (most recent call last): File ./scripts/migrate_tools/migrate_tools.py, line 21, in module app = MigrateToolsApplication( sys.argv[ 1 ] ) File /home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/migrate/common.py, line 76, in __init__ install_dependencies=install_dependencies ) File /home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py, line 75, in __init__ self.install_repository( repository_elem, install_dependencies ) File /home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py, line 319, in install_repository install_dependencies=install_dependencies ) File /home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py, line 203, in handle_repository_contents persist=True ) File /home/GLBRCORG/galaxy/galaxy-central/lib/tool_shed/util/metadata_util.py, line 594, in generate_metadata_for_changeset_revision tool, valid, error_message = tool_util.load_tool_from_config( app, app.security.encode_id( repository.id ), full_path ) AttributeError: 'MigrateToolsApplication' object has no attribute 'security' Any help would be greatly appreciated. Thanks! -- Branden Timm bt...@energy.wisc.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/ 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/
