October 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 09bc1f: Test mutable configs
by GitHub 28 Oct '15

28 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 09bc1f1098e93ba0d03a18b091e243a2ac7e1c96 https://github.com/galaxyproject/usegalaxy-playbook/commit/09bc1f1098e93ba0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Commit: ac7883fca092fc857e798dae8883bbc335662966 https://github.com/galaxyproject/usegalaxy-playbook/commit/ac7883fca092fc85… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: R roles/galaxyprojectdotorg.galaxy/tasks/eggs.yml Log Message: ----------- Removal missed in the galaxy role upgrade Commit: 0807be3e6d843330c3f045c64e060253d0743814 https://github.com/galaxyproject/usegalaxy-playbook/commit/0807be3e6d843330… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Disable OpenID on Test until #994 is merged Commit: 286ba22d5dc987abf30641f0c5cd25b46c8bc521 https://github.com/galaxyproject/usegalaxy-playbook/commit/286ba22d5dc987ab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-28 (Wed, 28 Oct 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ee079f369c5e...…

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[galaxyproject/galaxy] dc9c2e: Fix grid batch operations. This should correctly ...
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: dc9c2e4b7569726263fac8ab06cefb889c2b8af5 https://github.com/galaxyproject/galaxy/commit/dc9c2e4b7569726263fac8ab06ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix grid batch operations. This should correctly display and request confirmation for batch operations (such as delete a set of <GalaxyObjects> which is scary without a confirmation). It also fixes it to where grid bulk operations actually work in IE. Commit: 7bcbf140936bfc9d25b8e6bed8a0bc14270b0cf2 https://github.com/galaxyproject/galaxy/commit/7bcbf140936bfc9d25b8e6bed8a0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge pull request #978 from dannon/graft_to_stable [15.10] Fix grid bulk operations Compare: https://github.com/galaxyproject/galaxy/compare/dab1ce3f03c2...7bcbf140936b

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[galaxyproject/galaxy] 9563f1: binary_compatibility.py shouldn't fail on platform...
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9563f121e8d099315c75ce8d59c9b3d0d12fcbee https://github.com/galaxyproject/galaxy/commit/9563f121e8d099315c75ce8d59c9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- binary_compatibility.py shouldn't fail on platforms that don't return anything for get_specific_platform() (e.g. things other than Linux). Commit: 3529ef6b6e960ae5cbb12d415f468993e0585338 https://github.com/galaxyproject/galaxy/commit/3529ef6b6e960ae5cbb12d415f46… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #995 from natefoo/smash-eggs-bugfix1 binary_compatibility.py shouldn't fail Compare: https://github.com/galaxyproject/galaxy/compare/a71f504b1e9e...3529ef6b6e96

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[galaxyproject/galaxy] 291f4d: add google analytics tracking to newlibs, propagat...
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 291f4d77d62be708bd9ead6bfc546722eb2a66cf https://github.com/galaxyproject/galaxy/commit/291f4d77d62be708bd9ead6bfc54… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M lib/galaxy/managers/configuration.py M static/maps/galaxy.library.js.map M static/scripts/galaxy.library.js Log Message: ----------- add google analytics tracking to newlibs, propagate ga_code to JS config Commit: f0fbd25526032ce35c824c8e2af7f72794327707 https://github.com/galaxyproject/galaxy/commit/f0fbd25526032ce35c824c8e2af7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M CONTRIBUTING.md M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/library.less M client/galaxy/style/less/list-item.less M create_db.sh R dist-eggs.ini M doc/source/index.rst A doc/source/project/issues.rst R eggs.ini M lib/galaxy/__init__.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/util/gff_util.py A lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/dependencies/dev-requirements.txt A lib/galaxy/dependencies/requirements.txt M lib/galaxy/eggs/__init__.py R lib/galaxy/eggs/dist.py R lib/galaxy/eggs/scramble.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/template.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/util.py M lib/galaxy/workflow/render.py M lib/galaxy_ext/metadata/set_metadata.py R lib/pkg_resources.py M lib/pulsar/client/config_util.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M 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lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/search_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M manage_db.sh M manage_tools.sh M requirements.txt M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/common.py A scripts/binary_compatibility.py R scripts/check_eggs.py M scripts/check_galaxy.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/common_startup.sh M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py R scripts/dist-scramble.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py R scripts/egg_packager_template.py R scripts/fetch_eggs.py M scripts/functional_tests.py R scripts/make_egg_packager.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/nosetests.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py R scripts/scramble.py R scripts/scramble/lib/scramble_lib.py R scripts/scramble/patches/Cheetah/SetupConfig.py R scripts/scramble/patches/MySQL_python/site.cfg R scripts/scramble/patches/PasteScript/setup.py R scripts/scramble/patches/python_daemon/setup.py R scripts/scramble/scripts/DRMAA_python-macosx.py R scripts/scramble/scripts/DRMAA_python-solaris.py R scripts/scramble/scripts/DRMAA_python.py R scripts/scramble/scripts/MySQL_python-solaris.py R scripts/scramble/scripts/MySQL_python.py R scripts/scramble/scripts/PyRods.py R scripts/scramble/scripts/bx_python-solaris.py R scripts/scramble/scripts/generic.py R scripts/scramble/scripts/pbs_python.py R scripts/scramble/scripts/psycopg2-linux.py R scripts/scramble/scripts/psycopg2-macosx.py R scripts/scramble/scripts/psycopg2-solaris.py R scripts/scramble/scripts/psycopg2.py R scripts/scramble/scripts/pysam-solaris.py R scripts/scramble/scripts/pysqlite.py M scripts/summarize_timings.py R scripts/test_dist_egg.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M scripts/update_shed_config_path.py M set_metadata.sh M static/maps/libs/jquery/jquery.dynatree.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/reports_webapp/run_stats.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/list/list-panel.js M static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css R static/style/blue/dynatree_skin/cbChecked.gif R static/style/blue/dynatree_skin/cbChecked_hover.gif R static/style/blue/dynatree_skin/cbIntermediate.gif R static/style/blue/dynatree_skin/cbIntermediate_hover.gif R static/style/blue/dynatree_skin/cbUnchecked.gif R static/style/blue/dynatree_skin/cbUnchecked_hover.gif R static/style/blue/dynatree_skin/customDoc1.gif R static/style/blue/dynatree_skin/customFolder1.gif A static/style/blue/dynatree_skin/icons-rtl.gif A static/style/blue/dynatree_skin/icons.gif A static/style/blue/dynatree_skin/loading.gif R 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static/style/blue/dynatree_skin/ui.dynatree.css A static/style/blue/dynatree_skin/vline-rtl.gif A static/style/blue/dynatree_skin/vline.gif M static/style/blue/library.css M templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/base/base_panels.mako M templates/webapps/galaxy/root/index.mako M templates/webapps/tool_shed/repository/common.mako M test/base/instrument.py M test/base/interactor.py M test/base/nose_util.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/functional/test_metadata_editing.py M test/functional/tools/simple_constructs.yml M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/base/test_db_util.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_objectstore.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tools/filters/cutWrapper.xml M tools/genomespace/genomespace_importer.xml M tox.ini Log Message: ----------- Merge branch 'dev' into track-newlibs Conflicts: static/maps/galaxy.library.js.map static/scripts/galaxy.library.js Commit: a71f504b1e9e1b10a188804bc2c359218d815483 https://github.com/galaxyproject/galaxy/commit/a71f504b1e9e1b10a188804bc2c3… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M lib/galaxy/managers/configuration.py M static/maps/galaxy.library.js.map M static/scripts/galaxy.library.js Log Message: ----------- Merge pull request #959 from martenson/track-newlibs add google analytics tracking to newlibs, propagate ga_code to JS config Compare: https://github.com/galaxyproject/galaxy/compare/e31ec7b0c8bc...a71f504b1e9e

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[galaxyproject/usegalaxy-playbook] ee079f: Update galaxyprojectdotorg.galaxy to 0.6
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ee079f369c5e05952b006b73512bc431837ce58d https://github.com/galaxyproject/usegalaxy-playbook/commit/ee079f369c5e0595… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M roles/galaxyprojectdotorg.galaxy/README.md M roles/galaxyprojectdotorg.galaxy/defaults/main.yml M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/meta/main.yml M roles/galaxyprojectdotorg.galaxy/tasks/clone.yml A roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml Log Message: ----------- Update galaxyprojectdotorg.galaxy to 0.6

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[galaxyproject/ansible-galaxy]
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/tags/0.6 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] c2c4af: Ensure $VIRTUAL_ENV is always set when running pip...
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: c2c4afeb19d608ed381554ea943d2566ca14cd18 https://github.com/galaxyproject/ansible-galaxy/commit/c2c4afeb19d608ed3815… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M tasks/dependencies.yml Log Message: ----------- Ensure $VIRTUAL_ENV is always set when running pip (it is not activated, but reading binary-compatibility.cfg depends on it). Add a task for running Galaxy's binary_compatibility.py script so that CentOS can install RHEL wheels.

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[galaxyproject/galaxy] 9503f1: Fix the raven conditional requirement
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9503f1ddf3b6130eb9bf14cda057be21812b8ef2 https://github.com/galaxyproject/galaxy/commit/9503f1ddf3b6130eb9bf14cda057… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Fix the raven conditional requirement Commit: 1a3a594d4e397e11b3cb38a81add00b4482505ed https://github.com/galaxyproject/galaxy/commit/1a3a594d4e397e11b3cb38a81add… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-26 (Mon, 26 Oct 2015) Changed paths: A scripts/binary_compatibility.py M scripts/common_startup.sh Log Message: ----------- Allow CentOS to install RHEL wheels. Commit: e31ec7b0c8bc6abf4346e29b9d1eed4923916f25 https://github.com/galaxyproject/galaxy/commit/e31ec7b0c8bc6abf4346e29b9d1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M lib/galaxy/dependencies/__init__.py A scripts/binary_compatibility.py M scripts/common_startup.sh Log Message: ----------- Merge pull request #989 from natefoo/smash_eggs Add a script for creating binary-compatibility.cfg and run it from common_startup.sh Compare: https://github.com/galaxyproject/galaxy/compare/6d7be0a21868...e31ec7b0c8bc

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[galaxyproject/galaxy] f3bfa2: remove the autorefresh on Reports app
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3bfa2f56bb71f737ff8faa622271102652c7592 https://github.com/galaxyproject/galaxy/commit/f3bfa2f56bb71f737ff8faa62227… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- remove the autorefresh on Reports app because of how long each page takes on Main the request for a subpage would timeout because new autorefresh request would be automatically issued Commit: ee327702d75415261085796af1e5c1ff5b1308ee https://github.com/galaxyproject/galaxy/commit/ee327702d75415261085796af1e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix workflow extraction from history Fix history extraction by returning value dictionary Remove previous fix Commit: 9d3893ed632d95d8b70fdbc8a95ba9c44a9a5207 https://github.com/galaxyproject/galaxy/commit/9d3893ed632d95d8b70fdbc8a95b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Undo commit, wrong branch Commit: 8a0a445ec334d5c98ef601d80fff1bf111b6c453 https://github.com/galaxyproject/galaxy/commit/8a0a445ec334d5c98ef601d80fff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix workflow extraction from history Commit: 82e96140a17e75a0766c45a9071eb73d4b58a0e7 https://github.com/galaxyproject/galaxy/commit/82e96140a17e75a0766c45a9071e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Merge pull request #967 from martenson/remove-reports-autorefresh [15.10] remove the autorefresh on Reports app homepage Commit: 3fe148dd1981b516452df9ace6db75e95879df03 https://github.com/galaxyproject/galaxy/commit/3fe148dd1981b516452df9ace6db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #970 from guerler/fix_history_extract_001 [15.10] Fix workflow extraction from history Commit: 57d0620292d3272b3bd6f8f7e9ec3833931c62be https://github.com/galaxyproject/galaxy/commit/57d0620292d3272b3bd6f8f7e9ec… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Fix for missing included files on history export and import. Notes: If a history was exported previously, galaxy would just serve the cached version. In that case, it is better to make some changes to the history for example, by re-running the last job and then exporting it. Export of histories that haven't been exported previously should work without problems. (cherry picked from commit 9ea0fee48aa57361147e9145be8deaaafb2a0960) Commit: dfb59002ba78373dac32d8aebefd7b2de324260b https://github.com/galaxyproject/galaxy/commit/dfb59002ba78373dac32d8aebefd… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Use object store for imported history datasets and included files (cherry picked from commit ea89dd8f149778b6c2f0f3f4a34c8b21f7033af7) Commit: dab1ce3f03c25d35604d0ed75fc8aa6e3702c26d https://github.com/galaxyproject/galaxy/commit/dab1ce3f03c25d35604d0ed75fc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Merge pull request #973 from natefoo/composite-history-import-export [15.10] Fix for missing included files on history export and import Commit: 6d7be0a2186882c6090584a1cd58c59c18a0a519 https://github.com/galaxyproject/galaxy/commit/6d7be0a2186882c6090584a1cd58… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-27 (Tue, 27 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M lib/galaxy/tools/__init__.py M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Merge branch 'release_15.10' of https://github.com/galaxyproject/galaxy into dev Compare: https://github.com/galaxyproject/galaxy/compare/5f3fbdefbeb5...6d7be0a21868

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[galaxyproject/galaxy] f3bfa2: remove the autorefresh on Reports app
by GitHub 27 Oct '15

27 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: f3bfa2f56bb71f737ff8faa622271102652c7592 https://github.com/galaxyproject/galaxy/commit/f3bfa2f56bb71f737ff8faa62227… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- remove the autorefresh on Reports app because of how long each page takes on Main the request for a subpage would timeout because new autorefresh request would be automatically issued Commit: ee327702d75415261085796af1e5c1ff5b1308ee https://github.com/galaxyproject/galaxy/commit/ee327702d75415261085796af1e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix workflow extraction from history Fix history extraction by returning value dictionary Remove previous fix Commit: 9d3893ed632d95d8b70fdbc8a95ba9c44a9a5207 https://github.com/galaxyproject/galaxy/commit/9d3893ed632d95d8b70fdbc8a95b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Undo commit, wrong branch Commit: 8a0a445ec334d5c98ef601d80fff1bf111b6c453 https://github.com/galaxyproject/galaxy/commit/8a0a445ec334d5c98ef601d80fff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix workflow extraction from history Commit: 82e96140a17e75a0766c45a9071eb73d4b58a0e7 https://github.com/galaxyproject/galaxy/commit/82e96140a17e75a0766c45a9071e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Merge pull request #967 from martenson/remove-reports-autorefresh [15.10] remove the autorefresh on Reports app homepage Commit: 3fe148dd1981b516452df9ace6db75e95879df03 https://github.com/galaxyproject/galaxy/commit/3fe148dd1981b516452df9ace6db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #970 from guerler/fix_history_extract_001 [15.10] Fix workflow extraction from history Commit: 57d0620292d3272b3bd6f8f7e9ec3833931c62be https://github.com/galaxyproject/galaxy/commit/57d0620292d3272b3bd6f8f7e9ec… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Fix for missing included files on history export and import. Notes: If a history was exported previously, galaxy would just serve the cached version. In that case, it is better to make some changes to the history for example, by re-running the last job and then exporting it. Export of histories that haven't been exported previously should work without problems. (cherry picked from commit 9ea0fee48aa57361147e9145be8deaaafb2a0960) Commit: dfb59002ba78373dac32d8aebefd7b2de324260b https://github.com/galaxyproject/galaxy/commit/dfb59002ba78373dac32d8aebefd… Author: Vimalkumar Velayudhan <vimalkumarvelayudhan(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Use object store for imported history datasets and included files (cherry picked from commit ea89dd8f149778b6c2f0f3f4a34c8b21f7033af7) Commit: dab1ce3f03c25d35604d0ed75fc8aa6e3702c26d https://github.com/galaxyproject/galaxy/commit/dab1ce3f03c25d35604d0ed75fc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py Log Message: ----------- Merge pull request #973 from natefoo/composite-history-import-export [15.10] Fix for missing included files on history export and import Compare: https://github.com/galaxyproject/galaxy/compare/ab7ec7b3abbb...dab1ce3f03c2

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