- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] d1ea56: Dropped FROG; added Whale Shark to slide rotation.
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d1ea56bcd75e1dd116cb40e1e05466b32bb0498e https://github.com/galaxyproject/usegalaxy-playbook/commit/d1ea56bcd75e1dd1… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: A files/galaxy/common/static/welcome_img/WhaleSharkGalaxy.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped FROG; added Whale Shark to slide rotation.

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[galaxyproject/usegalaxy-playbook] 39697f: Send user emails to Pulsar
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 39697f3e0ace753a5eed10d3a47ed58290f5ed34 https://github.com/galaxyproject/usegalaxy-playbook/commit/39697f3e0ace753a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Send user emails to Pulsar

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[galaxyproject/usegalaxy-playbook] 6f88ff: Update Main Pulsar, so we can use the queued_drmaa...
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f88ffbe73cf9c28f3bfadf2853a64aad527e1a6 https://github.com/galaxyproject/usegalaxy-playbook/commit/6f88ffbe73cf9c28… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M production/group_vars/pulsarservers.yml M production/host_vars/login5.stampede.tacc.utexas.edu.yml A production/secret_host_vars/default.yml A production/secret_host_vars/login5.stampede.tacc.utexas.edu.yml R production/secret_vars/pulsarservers.yml Log Message: ----------- Update Main Pulsar, so we can use the queued_drmaa_xsede manager.

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[galaxyproject/usegalaxy-playbook] 01daf9: Don't put the entire Pulsar config in the vault.
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 01daf92372f9028d282cd652590ee5c020c1dc46 https://github.com/galaxyproject/usegalaxy-playbook/commit/01daf92372f9028d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M stage/host_vars/greenfield.psc.xsede.org.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml M stage/secret_host_vars/greenfield.psc.xsede.org.yml M stage/secret_host_vars/login5.stampede.tacc.utexas.edu.yml Log Message: ----------- Don't put the entire Pulsar config in the vault.

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[galaxyproject/usegalaxy-playbook] baace3: Mutable configs from Test
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: baace3cb279df293539f3bcee62930acfc4432b2 https://github.com/galaxyproject/usegalaxy-playbook/commit/baace3cb279df293… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml 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: ----------- Mutable configs from Test Commit: c6558da436bc254914626df09a2c11a38d27d84f https://github.com/galaxyproject/usegalaxy-playbook/commit/c6558da436bc2549… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml M files/galaxy/test.galaxyproject.org/config/tool_conf.xml R files/galaxy/test.galaxyproject.org/dynamic_rules/blacklight_select.py A files/galaxy/test.galaxyproject.org/dynamic_rules/greenfield_select.py R files/galaxy/test.galaxyproject.org/nagios/echo_test_blacklight.xml A files/galaxy/test.galaxyproject.org/nagios/echo_test_greenfield.xml M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M pulsar.yml M stage/group_vars/galaxyservers.yml M stage/group_vars/pulsarservers.yml M stage/host_vars/greenfield.psc.xsede.org.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml M stage/inventory A stage/secret_host_vars/default.yml A stage/secret_host_vars/greenfield.psc.xsede.org.yml A stage/secret_host_vars/login5.stampede.tacc.utexas.edu.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Update Pulsar on Test, move from Blacklight to Greenfield Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/437bc81f4346...…

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[galaxyproject/galaxy] f6b555: For CSV type data, do not fail to set metadata whe...
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: f6b5558c11698069c4eebb1b28f089a3ecc32c40 https://github.com/galaxyproject/galaxy/commit/f6b5558c11698069c4eebb1b28f0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- For CSV type data, do not fail to set metadata when header and data row column counts mismatch. Commit: 099d61ef21e9cf1eae364cf807aa7e3705d8d787 https://github.com/galaxyproject/galaxy/commit/099d61ef21e9cf1eae364cf807aa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix for raising error when trying to compare unknown column types in CSV. Commit: 566acab16e52d3e9a1969366a2a52e02bf8c1eb9 https://github.com/galaxyproject/galaxy/commit/566acab16e52d3e9a1969366a2a5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #680 from blankenberg/csv_fix [15.07] For CSV type data, do not fail to set metadata when header and data row column counts mismatch. Compare: https://github.com/galaxyproject/galaxy/compare/f4605937e3bb...566acab16e52

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[galaxyproject/galaxy] 15d9df: Managers, collections: return copied hdca from cop...
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 15d9dfd3073b8da1684b10ec489d9d7f0f6b5939 https://github.com/galaxyproject/galaxy/commit/15d9dfd3073b8da1684b10ec489d… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Managers, collections: return copied hdca from copy method Commit: d00b5507c0d33ea334ab9db5677b461b998c74ab https://github.com/galaxyproject/galaxy/commit/d00b5507c0d33ea334ab9db5677b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Merge pull request #682 from carlfeberhard/fix.copied-collection-hid Managers, collections: return copied hdca from copy method Compare: https://github.com/galaxyproject/galaxy/compare/c47d4a715ed4...d00b5507c0d3

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[galaxyproject/galaxy] 1b64be: API, histories: allow sorting by disk_size, move o...
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1b64bea779eab01a5a190d1f44707148b18e2d21 https://github.com/galaxyproject/galaxy/commit/1b64bea779eab01a5a190d1f4470… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- API, histories: allow sorting by disk_size, move order parsing into manager Commit: ea130e2c008e100de92da78fa62ac797b635baed https://github.com/galaxyproject/galaxy/commit/ea130e2c008e100de92da78fa62a… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Histories: move order parsing into managers; View multi: allow and pass ordering into bootstrapped histories, limit to 10; View multi, client: allow better collection setting and addition Commit: d8ee54251afbcb965c02af47d800fac1e005a004 https://github.com/galaxyproject/galaxy/commit/d8ee54251afbcb965c02af47d800… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M CONTRIBUTING.md M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/ui/ui-button-menu.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js R client/galaxy/scripts/mvc/upload/upload-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/reports.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/grunt-tasks/scripts.js M config/galaxy.ini.sample M doc/source/project/organization.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/sharable.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/galaxy/util/bunch.py M lib/galaxy/util/jstree.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/render.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/cleanup_datasets/cleanup_datasets.py R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/reports_webapp/bases/home-icon-active.png R static/images/reports_webapp/bases/home-icon-hov.png R static/images/reports_webapp/bases/home-icon.png R static/images/reports_webapp/home-icon-active.png R static/images/reports_webapp/home-icon-hov.png R static/images/reports_webapp/home-icon.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg M static/maps/galaxy.interactive_environments.js.map M static/maps/galaxy.menu.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-button-menu.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select.js.map A static/maps/mvc/upload/composite/composite-row.js.map A static/maps/mvc/upload/composite/composite-view.js.map A static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.menu.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-button-menu.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select.js A static/scripts/mvc/upload/composite/composite-row.js A static/scripts/mvc/upload/composite/composite-view.js A static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/reports_webapp/run_stats.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/reports.css R static/welcome.rst M templates/page_base.mako M templates/spark_base.mako R templates/webapps/galaxy/cloud/index.mako A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js M test/unit/test_galaxy_mapping.py M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample R tool-data/fastx_clipper_sequences.txt M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Merge remote-tracking branch 'origin/dev' into history.multi Commit: 15fe2b7d8ff79dfbc3ac2592246401b7c6c0af52 https://github.com/galaxyproject/galaxy/commit/15fe2b7d8ff79dfbc3ac25922464… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/utils/uploadbox.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, histories: lazy-load histories in the multi-history view, handle search loading indication better, move sort/comparator code into collection Commit: efc1df79f195d7479cc8a7dfb4f811e8ae82329b https://github.com/galaxyproject/galaxy/commit/efc1df79f195d7479cc8a7dfb4f8… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, histories: move load indicator style to less, use better name Commit: c47d4a715ed4acf2ed72693f9659730b402fd001 https://github.com/galaxyproject/galaxy/commit/c47d4a715ed4acf2ed72693f9659… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Merge pull request #676 from carlfeberhard/history.multi Lazy-load histories into multi-history view Compare: https://github.com/galaxyproject/galaxy/compare/0a1617024c79...c47d4a715ed4

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[galaxyproject/usegalaxy-playbook] 437bc8: Remove Dave and myself from reserved users list
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 437bc81f43466a8aeb922295953aa43b24dd12b3 https://github.com/galaxyproject/usegalaxy-playbook/commit/437bc81f43466a8a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py Log Message: ----------- Remove Dave and myself from reserved users list

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[galaxyproject/usegalaxy-playbook] 3d06c1: Update galaxyprojectdotorg.pulsar to 0.4.1.
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3d06c1cb102ba44ca2ac41f917f793f4ef3a6f7c https://github.com/galaxyproject/usegalaxy-playbook/commit/3d06c1cb102ba44c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M roles/galaxyprojectdotorg.pulsar/README.md M roles/galaxyprojectdotorg.pulsar/defaults/main.yml M roles/galaxyprojectdotorg.pulsar/meta/.galaxy_install_info M roles/galaxyprojectdotorg.pulsar/tasks/main.yml A stage/host_vars/greenfield.psc.xsede.org.yml R stage/host_vars/tg-login2.blacklight.psc.xsede.org.yml R stage/secret_vars/pulsarservers.yml Log Message: ----------- Update galaxyprojectdotorg.pulsar to 0.4.1.

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[galaxyproject/ansible-pulsar]
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/tags/0.4.1 Home: https://github.com/galaxyproject/ansible-pulsar

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[galaxyproject/ansible-pulsar] 5c7730: Add pip installability.
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-pulsar Commit: 5c7730f6c61fdd15bbd1f3caf4d13479ecd11266 https://github.com/galaxyproject/ansible-pulsar/commit/5c7730f6c61fdd15bbd1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M README.md M defaults/main.yml M tasks/main.yml Log Message: ----------- Add pip installability.

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[galaxyproject/usegalaxy-playbook] 1e0191: Update galaxyprojectdotorg.pulsar to 0.4
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1e0191231150412e2bdf1889bf70e60d67b4d481 https://github.com/galaxyproject/usegalaxy-playbook/commit/1e0191231150412e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M roles/galaxyprojectdotorg.pulsar/README.md M roles/galaxyprojectdotorg.pulsar/defaults/main.yml M roles/galaxyprojectdotorg.pulsar/meta/.galaxy_install_info M roles/galaxyprojectdotorg.pulsar/tasks/main.yml A roles/galaxyprojectdotorg.pulsar/templates/app.yml.j2 M roles/galaxyprojectdotorg.pulsar/templates/server.ini.j2 Log Message: ----------- Update galaxyprojectdotorg.pulsar to 0.4

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[galaxyproject/ansible-pulsar]
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/tags/0.4 Home: https://github.com/galaxyproject/ansible-pulsar

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[galaxyproject/ansible-pulsar] 511a68: Add support for app.yml
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-pulsar Commit: 511a682c6cf3d1ad0e2740c7b79b1e5ce79335c4 https://github.com/galaxyproject/ansible-pulsar/commit/511a682c6cf3d1ad0e27… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M README.md M tasks/main.yml A templates/app.yml.j2 M templates/server.ini.j2 Log Message: ----------- Add support for app.yml

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[galaxyproject/galaxy] 041c94: Release notes for 15.07.
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 041c94bf788bea0990401dab14e0ab717cec0c55 https://github.com/galaxyproject/galaxy/commit/041c94bf788bea0990401dab14e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M scripts/bootstrap_history.py Log Message: ----------- Release notes for 15.07. This includes a script to boot strap the notes for future releases, updated announcement page for 15.07, and new announcement page for 15.10. Commit: 4a05c07aa5cc8e386742bb638a6c44e839efc9bd https://github.com/galaxyproject/galaxy/commit/4a05c07aa5cc8e386742bb638a6c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A scripts/bootstrap_history_announce_template.rst Log Message: ----------- Fixup end of release items for release notes. Commit: 65f39b2eaf6b0c94b1044a92351c2b5799ca021a https://github.com/galaxyproject/galaxy/commit/65f39b2eaf6b0c94b1044a92351c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Typo noticed by @martenson. Commit: a460ebd7d6b6132fe00238e834dcff0efb449ad8 https://github.com/galaxyproject/galaxy/commit/a460ebd7d6b6132fe00238e834dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst Log Message: ----------- Fix for explicit markup ending without a blank line Commit: 51534edc63bb7758d4fb4a7aaec13df7a1e5e8eb https://github.com/galaxyproject/galaxy/commit/51534edc63bb7758d4fb4a7aaec1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Deprecation notice for cloudlaunch Commit: 96840a3c57354690b9287e49dd2ef3400932b52e https://github.com/galaxyproject/galaxy/commit/96840a3c57354690b9287e49dd2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #9 from dannon/rn Deprecation notice for cloudlaunch. Commit: 82794e7ee7a8a6793438bf2021079515445bb873 https://github.com/galaxyproject/galaxy/commit/82794e7ee7a8a6793438bf202107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Fix cloudlaunch link. Commit: 36d262d7c695ba06c32f5c495a0a3ceb62d57731 https://github.com/galaxyproject/galaxy/commit/36d262d7c695ba06c32f5c495a0a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #10 from dannon/rn Fix cloudlaunch link. Commit: f4605937e3bb1e0e993c66ac86deabff374034c4 https://github.com/galaxyproject/galaxy/commit/f4605937e3bb1e0e993c66ac86de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst Log Message: ----------- Merge pull request #642 from jmchilton/rn [15.07] Release notes for 15.07. Compare: https://github.com/galaxyproject/galaxy/compare/3653bf5e37b1...f4605937e3bb

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[galaxyproject/galaxy] 4dd630: Fix version parsing in tool form
by GitHub 31 Aug '15

31 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 4dd6304f055706e38176823a4166c6536618a042 https://github.com/galaxyproject/galaxy/commit/4dd6304f055706e38176823a4166… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Fix version parsing in tool form Commit: 3653bf5e37b13ea17cecd321fdbe9ce4fedcfbb8 https://github.com/galaxyproject/galaxy/commit/3653bf5e37b13ea17cecd321fdbe… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge pull request #677 from guerler/fix_version_002 [15.07] Fix version handling in tool form Compare: https://github.com/galaxyproject/galaxy/compare/525188d2a871...3653bf5e37b1

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[galaxyproject/infrastructure-playbook] 89b873: Update common_roles version
by GitHub 31 Aug '15

31 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 89b87312737d0756b16532c7cf140d8039b1747c https://github.com/galaxyproject/infrastructure-playbook/commit/89b87312737… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M common_roles Log Message: ----------- Update common_roles version Commit: 80a4025a60801b40dc46239ca16b39ec3cd756d0 https://github.com/galaxyproject/infrastructure-playbook/commit/80a4025a608… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: A galaxyenv/host_vars/n2.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_host_vars/default.yml A galaxyenv/secret_host_vars/n2.galaxyproject.org.yml M playbook.yml Log Message: ----------- Set up n2.galaxyproject.org for Jenkins. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/e997536619…

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[galaxyproject/galaxy] aa7968: Changed class naming to reflect use
by GitHub 31 Aug '15

31 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa7968aa9d13ab5de9fcebd427e5eca356cc1de4 https://github.com/galaxyproject/galaxy/commit/aa7968aa9d13ab5de9fcebd427e5… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/job_info.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Changed class naming to reflect use Commit: 0a1617024c7923c12531fa9e18da3494833a6f1f https://github.com/galaxyproject/galaxy/commit/0a1617024c7923c12531fa9e18da… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/job_info.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #675 from Airistotal/dev Changed class naming to reflect use Compare: https://github.com/galaxyproject/galaxy/compare/f61f696724a0...0a1617024c79

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[galaxyproject/galaxy] 469d8b: Fixed change in class overlap
by GitHub 31 Aug '15

31 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 469d8b463e4711770925f4152c95769b7c1d04dc https://github.com/galaxyproject/galaxy/commit/469d8b463e4711770925f4152c95… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Fixed change in class overlap Commit: ec8cba20398dcfe0fdd7a46ad93cf78fadc310ec https://github.com/galaxyproject/galaxy/commit/ec8cba20398dcfe0fdd7a46ad93c… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M client/galaxy/style/less/reports.less A doc/source/api/quickstart.rst M doc/source/api_doc.rst A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst M doc/source/ts_api_doc.rst M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/shed_util_common.py M test/base/asserts/__init__.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.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/functional/test_install_repositories.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/qunit/README.txt M test/qunit/package.json M test/unit/managers/test_DatasetManager.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Conflicts: client/galaxy/style/less/reports.less static/style/blue/base.css static/style/blue/reports.css Commit: f61f696724a0b264a8706d6bf682fa09c178bc5e https://github.com/galaxyproject/galaxy/commit/f61f696724a0b264a8706d6bf682… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #669 from Airistotal/dev Fix centering bug in firefox Compare: https://github.com/galaxyproject/galaxy/compare/d4af323d35e4...f61f696724a0

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[galaxyproject/galaxy] 8cd94b: When uploading tool_dependencies.xml to toolshed, ...
by GitHub 28 Aug '15

28 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 8cd94be52d5030634e843a89d7025ecb6f18394b https://github.com/galaxyproject/galaxy/commit/8cd94be52d5030634e843a89d702… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- When uploading tool_dependencies.xml to toolshed, do set toolshed repository attributes of package/repository tags that occur within actions that specify os or architecture. Commit: 525188d2a871fbb9b5e7438b18bb5412f62db975 https://github.com/galaxyproject/galaxy/commit/525188d2a871fbb9b5e7438b18bb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- Merge pull request #637 from blankenberg/recurse-toolshed-changeset-upload [release_15.07] Fix setting of toolshed repository attributes in special cases. Compare: https://github.com/galaxyproject/galaxy/compare/4fcdf9fda1d2...525188d2a871

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[galaxyproject/galaxy] 0fa73f: Don't overwrite $R_LIBS path during installation.
by GitHub 28 Aug '15

28 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0fa73f2a81fed31fbfe778cf2197d46fa0d4f899 https://github.com/galaxyproject/galaxy/commit/0fa73f2a81fed31fbfe778cf2197… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Don't overwrite $R_LIBS path during installation. Commit: d4af323d35e4a562c6f676ebf10e63253e4d53f8 https://github.com/galaxyproject/galaxy/commit/d4af323d35e4a562c6f676ebf10e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #671 from bgruening/extend_r_libs_path Don't overwrite $R_LIBS path during installation. Compare: https://github.com/galaxyproject/galaxy/compare/eae62ca2cb12...d4af323d35e4

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[galaxyproject/usegalaxy-playbook] fb77a4: update TTS
by GitHub 28 Aug '15

28 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fb77a413a334a7974a582af4e13aa285469356b2 https://github.com/galaxyproject/usegalaxy-playbook/commit/fb77a413a334a797… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/galaxy] f28ddf: Use new path variable syntax available since Route...
by GitHub 28 Aug '15

28 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f28ddf779cc18ae87eff2c1d28c65622e367dbfb https://github.com/galaxyproject/galaxy/commit/f28ddf779cc18ae87eff2c1d28c6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Use new path variable syntax available since Routes 1.9 The old syntax is now documented only in the "Backward compatibility" section of Routes documentation. It is still supported, but may be removed in the future. Commit: eae62ca2cb122f5a0a674027fadc0a28d9dd179e https://github.com/galaxyproject/galaxy/commit/eae62ca2cb122f5a0a674027fadc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #665 from nsoranzo/dev Use new path variable syntax available since Routes 1.9 Compare: https://github.com/galaxyproject/galaxy/compare/bada494b85c9...eae62ca2cb12

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[galaxyproject/galaxy] 7ce4bd: Allow accessing repeat and conditional elements in...
by GitHub 27 Aug '15

27 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ce4bde8781645b09bb7ce54b9b7114c41ff9c36 https://github.com/galaxyproject/galaxy/commit/7ce4bde8781645b09bb7ce54b9b7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Allow accessing repeat and conditional elements in PJA parameters. Use . instead of the | that would be the actual association name. Cannot use | because it is treated as a special character in this code. Parameters with . in the names break Galaxy in subtle ways anyway and so treating them as a special character here should not be a problem. Commit: bada494b85c93c5662275ab5652e29e7bfb9a0ac https://github.com/galaxyproject/galaxy/commit/bada494b85c93c5662275ab5652e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #662 from jmchilton/repeat_rename Allow accessing repeat and conditional elements in PJA parameters. Compare: https://github.com/galaxyproject/galaxy/compare/396bcc782082...bada494b85c9

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