Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84ad9c2ee2c5cf0420f837405dfbd1893f1d0ed2 https://github.com/galaxyproject/galaxy/commit/84ad9c2ee2c5cf0420f837405dfbd... Author: John Chilton <jmchilton@gmail.com> Date: 2016-04-10 (Sun, 10 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Rev Pulsar to 0.7.0.dev3. - Fixes numerous problems mostly notably fixes external metadata generation and job metrics collection for recent Pulsar. This was broken when tools were given clean working directory. - Produce a new message if an older Pulsar version is targetted via REST of library (should help with upgrading to Galaxy 16.04). - Newer pulsar lib allows more flexible configuration of managers - update documntation to reflect this. Commit: 27f418c52d685d41646fa6cf932e8144fef63bb5 https://github.com/galaxyproject/galaxy/commit/27f418c52d685d41646fa6cf932e8... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R install_and_test_tool_shed_repositories.sh R scripts/tool_shed/check_repositories_for_functional_tests.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py Log Message: ----------- Remove scripts which depend on install_and_test_tool_shed_repositories. Commit: a9d675f5e854de8634789fca54bb88c6a9f5de2c https://github.com/galaxyproject/galaxy/commit/a9d675f5e854de8634789fca54bb8... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Fix sys.path.insert() after #2093. Commit: ceeb01d84e7f510fab39626dec7f7d537a66f2fd https://github.com/galaxyproject/galaxy/commit/ceeb01d84e7f510fab39626dec7f7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: R install_and_test_tool_shed_repositories.sh M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Merge pull request #2133 from nsoranzo/release_16.04_fix_for_2093 [16.04] Fixes due to #2093 and #2018 Commit: f03c0375566a835b9e75135ba9462ddad1dfeb70 https://github.com/galaxyproject/galaxy/commit/f03c0375566a835b9e75135ba9462... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #2122 from jmchilton/pulsar_metadata [16.04] Rev Pulsar to 0.7.0.dev3. Commit: 408827e251f92cdc5b6c794272a6ba2dc1473780 https://github.com/galaxyproject/galaxy/commit/408827e251f92cdc5b6c794272a6b... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced R install_and_test_tool_shed_repositories.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/baf1bd639f17...408827e251f9