June 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 268ee7: Improve resilience of tool url building
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 268ee7f1b7e65dde514098e0779b80b7589d26b5 https://github.com/galaxyproject/galaxy/commit/268ee7f1b7e65dde514098e0779b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Improve resilience of tool url building Commit: 69e76f98fa90782c37a2697de0204e4ff7945f09 https://github.com/galaxyproject/galaxy/commit/69e76f98fa90782c37a2697de020… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Remove redundancy of tool_id parameter Commit: a498390bef74301816945551a9832f38747fd4fc https://github.com/galaxyproject/galaxy/commit/a498390bef74301816945551a983… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix basic version changes for reloaded tools Commit: 9dca211e2fe59eaad1f7b95c8d51608b2afa05af https://github.com/galaxyproject/galaxy/commit/9dca211e2fe59eaad1f7b95c8d51… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #4214 from guerler/revise_tool_url [17.05] Improve resilience of tool url building Compare: https://github.com/galaxyproject/galaxy/compare/f7ba7295102c...9dca211e2fe5

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[galaxyproject/usegalaxy-playbook] 8ae4c0: Data rewrites for Bridges on Main
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8ae4c0768d9e012e329cc71bd0d64eadba174a8b https://github.com/galaxyproject/usegalaxy-playbook/commit/8ae4c0768d9e012e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: A files/galaxy/usegalaxy.org/config/pulsar_bridges_actions.yml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M production/group_vars/galaxyservers.yml Log Message: ----------- Data rewrites for Bridges on Main

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[galaxyproject/usegalaxy-playbook] c06cee: Run RNA Star on Bridges on Test, configure data pa...
by GitHub 22 Jun '17

22 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c06cee0e218843b77ca86bab23007f16cfaa106a https://github.com/galaxyproject/usegalaxy-playbook/commit/c06cee0e218843b7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/bridges_select.py A env/test/files/galaxy/config/pulsar_bridges_actions.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run RNA Star on Bridges on Test, configure data path rewrites.

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[galaxyproject/usegalaxy-playbook] 3fbe6d: Run RNA Star on multi partition on TEst
by GitHub 21 Jun '17

21 Jun '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3fbe6d1d53f295cbe7b7a877db72d4a4c706ec4c https://github.com/galaxyproject/usegalaxy-playbook/commit/3fbe6d1d53f295cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run RNA Star on multi partition on TEst

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[galaxyproject/galaxy] 490d73: Fix left/right panel hiding
by GitHub 21 Jun '17

21 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 490d738ba4efea392297941ceb266fa428ca2323 https://github.com/galaxyproject/galaxy/commit/490d738ba4efea392297941ceb26… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Fix left/right panel hiding Commit: ecdaa04dfd14c1497f3db85409b4c0add8c91022 https://github.com/galaxyproject/galaxy/commit/ecdaa04dfd14c1497f3db85409b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #4210 from guerler/fix_panel_hiding Fix left/right panel hiding Compare: https://github.com/galaxyproject/galaxy/compare/9b9e2aa22742...ecdaa04dfd14

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[galaxyproject/galaxy] a407a9: Removing run mako from workflows
by GitHub 20 Jun '17

20 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a407a99ae3b8a83879b5f4629c8c07d7cfa3945b https://github.com/galaxyproject/galaxy/commit/a407a99ae3b8a83879b5f4629c8c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-29 (Mon, 29 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/workflow/workflow.js R templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Removing run mako from workflows Commit: 094dbe92c3e33d0184cc3691f3d9f66cb7e2b697 https://github.com/galaxyproject/galaxy/commit/094dbe92c3e33d0184cc3691f3d9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Adding basic elements for import workflow Commit: 6dba0c74f266483ef0a67d5d8f25f5ced1bbed37 https://github.com/galaxyproject/galaxy/commit/6dba0c74f266483ef0a67d5d8f25… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/configure_menu.mako Log Message: ----------- Merging with dev Commit: 764933bf3417c734ee2f5554ae122ddca1f3655a https://github.com/galaxyproject/galaxy/commit/764933bf3417c734ee2f5554ae12… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Adding import functionality Commit: 62bd742808e5c45a00cb64ac7ef962f936e57351 https://github.com/galaxyproject/galaxy/commit/62bd742808e5c45a00cb64ac7ef9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Moving common functions out of view and adding messages for client actions for importing workflow Commit: 07ea4c04347956fd5e177b052c86a63568aa28a7 https://github.com/galaxyproject/galaxy/commit/07ea4c04347956fd5e177b052c86… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M client/webpack.config.js M config/job_conf.xml.sample_advanced M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/dev/build_a_job_runner.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M 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.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst A doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.webhooks.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/psyco_full.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst M doc/source/releases/13.01_announce.rst M doc/source/releases/13.02_announce.rst M doc/source/releases/13.04_announce.rst M doc/source/releases/13.06_announce.rst M doc/source/releases/13.08_announce.rst M doc/source/releases/13.11_announce.rst M 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lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/compression_utils.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M static/welcome.html.sample M templates/grid_base.mako R templates/webapps/galaxy/page/list_published.mako M test/api/test_dataset_collections.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Resolving conflicts and merging with dev Commit: 207249a4665470288fe77ae9d532e3cb07d4ce32 https://github.com/galaxyproject/galaxy/commit/207249a4665470288fe77ae9d532… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Moving configure menu call to user preferences Commit: 77327d27b5f526f0b1ddd4375d32e57e83453169 https://github.com/galaxyproject/galaxy/commit/77327d27b5f526f0b1ddd4375d32… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: R templates/webapps/galaxy/workflow/import.mako Log Message: ----------- Removing import.mako file Commit: 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test/qunit/tests/ui_tests.js A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merging with dev Commit: 1caf29d7591ff3787de330de58003fd9f0c0b6e1 https://github.com/galaxyproject/galaxy/commit/1caf29d7591ff3787de330de5800… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Removing extra link for custom_builds in analysis.js Commit: 3573f4d59f3d177a0b91b06ce192e1711aaf4a0d https://github.com/galaxyproject/galaxy/commit/3573f4d59f3d177a0b91b06ce192… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Removing usused imports in workflow.js Commit: 785e3e557aeee7071905f1aa3d88c1ae1653ec9b https://github.com/galaxyproject/galaxy/commit/785e3e557aeee7071905f1aa3d88… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-09 (Fri, 09 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js Log Message: ----------- Fixing PR review comments Commit: b52042ef8ebe250a1124071a98f4de486e5dc737 https://github.com/galaxyproject/galaxy/commit/b52042ef8ebe250a1124071a98f4… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-09 (Fri, 09 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/page/page-list.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/page.py M static/maps/layout/menu.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/page/page-list.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/page/page-list.js M templates/sharing_base.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako Log Message: ----------- Merging with dev Commit: 5cc46a95c9c9a54ae390496b52c7efc8ac25cf0d https://github.com/galaxyproject/galaxy/commit/5cc46a95c9c9a54ae390496b52c7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-10 (Sat, 10 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fixing PR review comments Commit: 6d9a911ea9200d3339635c0f4370f18001271f8b https://github.com/galaxyproject/galaxy/commit/6d9a911ea9200d3339635c0f4370… Author: anuprulez 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lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js R templates/webapps/galaxy/dataset/grid.mako A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merging with dev Commit: 659c039601a474eba86156a6957dd48560630fa1 https://github.com/galaxyproject/galaxy/commit/659c039601a474eba86156a6957d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/style/less/base.less M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css Log Message: ----------- Revise panel/iframe handling, align naming, rely on empty to trigger removal of previous view Repack Move inline styles, use consistent naming Commit: 2c4c7147e075f036ee703a89eb6de7f39c4e10dd https://github.com/galaxyproject/galaxy/commit/2c4c7147e075f036ee703a89eb6d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Revise and fix resize handler Commit: 21312138a47cb0c3f958c318500937b11df31d49 https://github.com/galaxyproject/galaxy/commit/21312138a47cb0c3f958c3185009… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix deferred form destructor Commit: 71498cabfdb9e988e3035915a8be647b88db1ef8 https://github.com/galaxyproject/galaxy/commit/71498cabfdb9e988e3035915a8be… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix log statement Commit: d031758d7323c39ed3176c158355f9d697266ef1 https://github.com/galaxyproject/galaxy/commit/d031758d7323c39ed3176c158355… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Pack scripts Commit: f4e4c08bab6b8ecf39a69844a904e2fa1c3e4459 https://github.com/galaxyproject/galaxy/commit/f4e4c08bab6b8ecf39a69844a904… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/base.less M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css Log Message: ----------- Merge pull request #36 from guerler/fix_cleanup Fixes deferred removal of previous views, augments center panel handling Commit: 837a5c85fcf9c6906843fe413aaf10f27ef21af4 https://github.com/galaxyproject/galaxy/commit/837a5c85fcf9c6906843fe413aaf… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Merging changes with static files Commit: 8a09836ba79e7f7b08f51a8d7db7c416b03bd44f https://github.com/galaxyproject/galaxy/commit/8a09836ba79e7f7b08f51a8d7db7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M lib/galaxy/config.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/webapps/galaxy/api/webhooks.py M scripts/api/library_upload_dir.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- Merging with dev Commit: 9b9e2aa2274202c9afe336724c78142408c94a77 https://github.com/galaxyproject/galaxy/commit/9b9e2aa2274202c9afe336724c78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/user/user-preferences.js M 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static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge remote-tracking branch 'bgruening/convertworkflowmako' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6a0401e08ebc...9b9e2aa22742

1 0

[galaxyproject/galaxy] 325863: Add histories route to analaysis app
by GitHub 20 Jun '17

20 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3258635c159acfa3cd4ab33e1484b20b9bced9c1 https://github.com/galaxyproject/galaxy/commit/3258635c159acfa3cd4ab33e1484… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Add histories route to analaysis app Commit: 0fa6f144d013ecac7bcd268f100b07c2c7811ffe https://github.com/galaxyproject/galaxy/commit/0fa6f144d013ecac7bcd268f100b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/layout/menu.js Log Message: ----------- Redirect masthead link Commit: 15206d1dec8547b0ee23a5f8412478f79a6689e0 https://github.com/galaxyproject/galaxy/commit/15206d1dec8547b0ee23a5f84124… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add client route to backend app Commit: 6af0126e60fcffc8afa3d57c8a1d9490822bdfa4 https://github.com/galaxyproject/galaxy/commit/6af0126e60fcffc8afa3d57c8a1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Change controller response from mako to json Commit: 658483ba5e50516d3bbef8f22411534a483a1aa6 https://github.com/galaxyproject/galaxy/commit/658483ba5e50516d3bbef8f22411… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Fix refresh handler Commit: 23d086a9894d6ea67bf19ca0f74147f62e76c801 https://github.com/galaxyproject/galaxy/commit/23d086a9894d6ea67bf19ca0f741… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix sharing operation Commit: d7d33323952d81352259bc745d749b8583a3cd16 https://github.com/galaxyproject/galaxy/commit/d7d33323952d81352259bc745d74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove custom mako name from definition Commit: 9ed0326b150e71b781994c4d2def42f71fdb48d0 https://github.com/galaxyproject/galaxy/commit/9ed0326b150e71b781994c4d2def… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix rename operation Commit: c987e5fa375ce66f383482a7b30c23e71610d2a2 https://github.com/galaxyproject/galaxy/commit/c987e5fa375ce66f383482a7b30c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Revise view operation Commit: 843ed9e6a9d2f7545919b71b057068ffb52f4d01 https://github.com/galaxyproject/galaxy/commit/843ed9e6a9d2f7545919b71b0570… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Pack Commit: 49ae97d3a368d1352f591a8d5a6bde96307af27d https://github.com/galaxyproject/galaxy/commit/49ae97d3a368d1352f591a8d5a6b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove uncommented copy statement Commit: 0fb1059bf74bbd4ba7f12cdd0f1104141242290b https://github.com/galaxyproject/galaxy/commit/0fb1059bf74bbd4ba7f12cdd0f11… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako Log Message: ----------- Insert custom history-list view to accomodate copy dialog hack Commit: 01cab673e7dcca0e7d463e3aa4982e49fa632e27 https://github.com/galaxyproject/galaxy/commit/01cab673e7dcca0e7d463e3aa498… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: A static/maps/mvc/history/history-list.js.map A static/scripts/mvc/history/history-list.js Log Message: ----------- Add packed files Commit: e3a4bf5d9ed02fe22a6732637511490d0a086f8d https://github.com/galaxyproject/galaxy/commit/e3a4bf5d9ed02fe22a6732637511… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: A client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Add history list module Commit: 84adc659bc67b6b65206ad7f9e9ee10916237f30 https://github.com/galaxyproject/galaxy/commit/84adc659bc67b6b65206ad7f9e9e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-list.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js Log Message: ----------- Augment grid view event handler to allow custom client side operations Commit: d931df2ca9d107d07af1c97a3d5de326f8ef378b https://github.com/galaxyproject/galaxy/commit/d931df2ca9d107d07af1c97a3d5d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M static/maps/mvc/history/history-list.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-list.js Log Message: ----------- Reimplement copy operation Commit: c3305581426fc2b344499079a5f94a65c9f5400a https://github.com/galaxyproject/galaxy/commit/c3305581426fc2b344499079a5f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Reroute link form history panel to saved grids Commit: 72d038504128a5b8e7ce721375b254b18805c450 https://github.com/galaxyproject/galaxy/commit/72d038504128a5b8e7ce721375b2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-07 (Wed, 07 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Fix target handling Commit: b9461eba40fbc3e8d3129fff94b954f2618c5ddf https://github.com/galaxyproject/galaxy/commit/b9461eba40fbc3e8d3129fff94b9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/page/page-list.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/text.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/mulled/util.py A lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M static/maps/layout/menu.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/page/page-list.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/page/page-list.js M templates/sharing_base.mako R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into grid_histories Commit: c2ebb5776bc26d62179fbc7ffe07bb7bec4288cf https://github.com/galaxyproject/galaxy/commit/c2ebb5776bc26d62179fbc7ffe07… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use explicit routes Commit: 434d944e5da46cf889b74a6759f3cce88c2f6aa4 https://github.com/galaxyproject/galaxy/commit/434d944e5da46cf889b74a6759f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/webapps/galaxy/api/webhooks.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- Merge branch 'dev' into grid_histories Commit: 6a0401e08ebce9797901812c57d7fca69a887c0b https://github.com/galaxyproject/galaxy/commit/6a0401e08ebce9797901812c57d7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/layout/menu.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/options-menu.js R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako Log Message: ----------- Merge pull request #4167 from guerler/grid_histories Remove histories grid mako Compare: https://github.com/galaxyproject/galaxy/compare/89851e4c7154...6a0401e08ebc

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[galaxyproject/galaxy] 76c6b6: Fix mulled Docker resolution.
by GitHub 19 Jun '17

19 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76c6b6f5bae1fbf7b2b564ecdb46a556590a6daa https://github.com/galaxyproject/galaxy/commit/76c6b6f5bae1fbf7b2b564ecdb46… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix mulled Docker resolution. I broke a bunch of Docker stuff when I abstracted it out for Singularity - things like ignoring namespaces because Singularity doesn't use that concept. Also fetching mulled-v2 images from quay.io was broken - I didn't notice this because previously there were no published images mulit-container images. Commit: ea1cf742f0f8e2f6277762c540e0173dbaf45964 https://github.com/galaxyproject/galaxy/commit/ea1cf742f0f8e2f6277762c540e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Bring in Singularity fixes from galaxy-lib. xref https://github.com/galaxyproject/galaxy-lib/pull/67 Commit: 89851e4c7154b451c02f83e1561a65ded45ae502 https://github.com/galaxyproject/galaxy/commit/89851e4c7154b451c02f83e1561a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Merge pull request #4207 from jmchilton/mulled_container_fixes Various mulled container fixes. Compare: https://github.com/galaxyproject/galaxy/compare/2a5dc90003c6...89851e4c7154

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[galaxyproject/galaxy] b32c1c: Check name export in legacy export section
by GitHub 19 Jun '17

19 Jun '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: b32c1cf1a3143804b0c4f12f6f7235a87801a74d https://github.com/galaxyproject/galaxy/commit/b32c1cf1a3143804b0c4f12f6f72… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Check name export in legacy export section Commit: f7ba7295102c9ce9969c634ee89e26f02c2801ea https://github.com/galaxyproject/galaxy/commit/f7ba7295102c9ce9969c634ee89e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4203 from guerler/fix_name_export [17.05] Check name type in legacy export section Compare: https://github.com/galaxyproject/galaxy/compare/d39b955e8a5d...f7ba7295102c

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[galaxyproject/infrastructure-playbook] 8c4b4f: Add singularity user to orval
by GitHub 19 Jun '17

19 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8c4b4fe9ae5908dc02e0da65d523f55d3e345140 https://github.com/galaxyproject/infrastructure-playbook/commit/8c4b4fe9ae5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M galaxyenv/host_vars/orval.galaxyproject.org.yml M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Add singularity user to orval

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