Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77706a8e62f6c7ffafc923b9f94f3359089e8ee9 https://github.com/galaxyproject/galaxy/commit/77706a8e62f6c7ffafc923b9f94f3... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.authnz.rst M doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.rst R doc/source/lib/galaxy.external_services.result_handlers.rst R doc/source/lib/galaxy.external_services.rst R doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst R doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.error_reports.plugins.rst A doc/source/lib/galaxy.tools.error_reports.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.verify.rst R doc/source/lib/galaxy.util.backports.rst R doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.logging.rst A doc/source/lib/galaxy.util.path.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.plugins.rst R doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst A doc/source/lib/galaxy.webapps.reports.framework.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.workflow.resources.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/tool_shed.util.rst Log Message: ----------- Update application documentation With ``` make -C doc/ updaterst ``` Commit: ad02c53154a3d3046a814b838cffdf0a79ac9a13 https://github.com/galaxyproject/galaxy/commit/ad02c53154a3d3046a814b838cffd... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/error_report.yml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst M doc/source/admin/config.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/releases/16.04_announce.rst M doc/source/releases/16.10.rst M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/search.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M run_tests.sh M scripts/api/README M scripts/slideshow/example.md M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/base/workflows_format_2/interface.py Log Message: ----------- Fix many links Commit: 59c1ed2266504a2bd03e80e9f4ec72664148524f https://github.com/galaxyproject/galaxy/commit/59c1ed2266504a2bd03e80e9f4ec7... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/galaxy.yml.sample M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/galaxy_options.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Various doc fixes Commit: b9d07aed22c59c2aeb92e30d18953bc6fecea0a6 https://github.com/galaxyproject/galaxy/commit/b9d07aed22c59c2aeb92e30d18953... Author: John Chilton <jmchilton@gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/error_report.yml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst M doc/source/admin/config.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.authnz.rst M doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.rst R doc/source/lib/galaxy.external_services.result_handlers.rst R doc/source/lib/galaxy.external_services.rst R doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst R doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.error_reports.plugins.rst A doc/source/lib/galaxy.tools.error_reports.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.verify.rst R doc/source/lib/galaxy.util.backports.rst R doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.logging.rst A doc/source/lib/galaxy.util.path.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.plugins.rst R doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst A doc/source/lib/galaxy.webapps.reports.framework.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.workflow.resources.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/tool_shed.util.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.10.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/search.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M run_tests.sh M scripts/api/README M scripts/slideshow/example.md M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/base/workflows_format_2/interface.py Log Message: ----------- Merge pull request #6662 from nsoranzo/doc_fixes2 Various link and documentation fixes Compare: https://github.com/galaxyproject/galaxy/compare/76d89d020f56...b9d07aed22c5 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.