- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f7ffde: Alias btn-xs to btn-sm for thinks (like welcome) w...
by GitHub 08 Jun '18

08 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f7ffde9db447be807f3c7924bbfe243c3f6faa51 https://github.com/galaxyproject/galaxy/commit/f7ffde9db447be807f3c7924bbfe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Alias btn-xs to btn-sm for thinks (like welcome) which may have been customized and rely on the previous styles. Commit: db444455b29b008b0f3bdf0844f38a4db1e457ef https://github.com/galaxyproject/galaxy/commit/db444455b29b008b0f3bdf0844f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Alias btn-default to btn-secondary for backwards compatibility. Commit: 074ec18490e2fb86c17a506374d78269c29ae03f https://github.com/galaxyproject/galaxy/commit/074ec18490e2fb86c17a506374d7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tours.js M static/style/blue/base.css Log Message: ----------- Missed label->badge translations. Commit: 69c74d52d4a4614aa544abd2c7a810fa817b7404 https://github.com/galaxyproject/galaxy/commit/69c74d52d4a4614aa544abd2c7a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tours.js M static/style/blue/base.css Log Message: ----------- Drop sm-badge-pad completely (standard styles handle this now) Commit: 20cf8b5bf0f4632d0f3c275c3261f920bbf76211 https://github.com/galaxyproject/galaxy/commit/20cf8b5bf0f4632d0f3c275c3261… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tours.js M static/style/blue/base.css Log Message: ----------- Merge pull request #6226 from dannon/minor_style_fixes [18.05] Two minor aliases for (exterior) backwards compatibility, minor badge tweaks Compare: https://github.com/galaxyproject/galaxy/compare/75c9610fdaf1...20cf8b5bf0f4 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f35c1d: Overhaul workflow execution response, including ap...
by GitHub 08 Jun '18

08 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f35c1d6630961f6ae5e9393ebd1504831765bcf8 https://github.com/galaxyproject/galaxy/commit/f35c1d6630961f6ae5e9393ebd15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Overhaul workflow execution response, including appropriate text for new histories, and multiple executions. With links. Commit: 75c9610fdaf1a59806e75458e04f1319e95f5a40 https://github.com/galaxyproject/galaxy/commit/75c9610fdaf1a59806e75458e04f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #6243 from dannon/workflow_submit_text_backport [18.05] Backport of Workflow Execution Text Fixup Compare: https://github.com/galaxyproject/galaxy/compare/f1adf0a79207...75c9610fdaf1 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 462909: Fix history list bottom border
by GitHub 08 Jun '18

08 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 46290939092a8068836712176ddbfc7641f69ada https://github.com/galaxyproject/galaxy/commit/46290939092a8068836712176ddb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix history list bottom border Commit: 7e220205f38abbe6d44f93f5ccfb14506838118a https://github.com/galaxyproject/galaxy/commit/7e220205f38abbe6d44f93f5ccfb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/history.scss Log Message: ----------- A more accurate version of what was set before, with the same outcome (though, it could change if we toggle the grey) Commit: cf3ed04d742938de52c24386dcf2f0c10409df71 https://github.com/galaxyproject/galaxy/commit/cf3ed04d742938de52c24386dcf2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix dataset messagesmall display, was a TODO left from migration Commit: 6cf4c8e5f4780421dc45472bf495694dd49aaa47 https://github.com/galaxyproject/galaxy/commit/6cf4c8e5f4780421dc45472bf495… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix one more busted fade Commit: 77dff21bcc6c1b2f93d400307a7f3332772f9943 https://github.com/galaxyproject/galaxy/commit/77dff21bcc6c1b2f93d400307a7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix (ancient, should replace this, but might as well make it work until we do) tool-shed-only grid search button Commit: 361b48a4d22e0f61ac6dcdf0d306d17d89b9d166 https://github.com/galaxyproject/galaxy/commit/361b48a4d22e0f61ac6dcdf0d306… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako Log Message: ----------- Drop submit-image custom styling, use standard fa; left it as inline style to keep it clean and remove all at once when this grid goes. Commit: 9fe40db5b3cf82f09ae3a783a8b708e78239f27f https://github.com/galaxyproject/galaxy/commit/9fe40db5b3cf82f09ae3a783a8b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix list panel control message margins. Commit: 0e39cf1924cfacb879802934da0112470cba9a0e https://github.com/galaxyproject/galaxy/commit/0e39cf1924cfacb879802934da01… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- This is correct now Commit: 18ae4457a131948fe87b7038215e81dec647e3db https://github.com/galaxyproject/galaxy/commit/18ae4457a131948fe87b7038215e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss Log Message: ----------- Formatting for styles and a couple misc files Commit: f1adf0a7920720ea7f20cdc3a21ea014f9ddd699 https://github.com/galaxyproject/galaxy/commit/f1adf0a7920720ea7f20cdc3a21e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako Log Message: ----------- Merge pull request #6238 from dannon/1805stylefixes_rebased [18.05] Various style fixes for history, toolshed, messages (backport) Compare: https://github.com/galaxyproject/galaxy/compare/12f51a47897f...f1adf0a79207 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 753ecd: Increase sleep if encountering exception
by GitHub 08 Jun '18

08 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 753ecd625c1410a3a6dc2c4a30e3f81fb71be29e https://github.com/galaxyproject/galaxy/commit/753ecd625c1410a3a6dc2c4a30e3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Increase sleep if encountering exception Commit: 12f51a47897faf55461626a504b61fa2793777d6 https://github.com/galaxyproject/galaxy/commit/12f51a47897faf55461626a504b6… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #6304 from mvdbeek/sleep_more [18.05] Increase sleep if encountering (DB locking) exception Compare: https://github.com/galaxyproject/galaxy/compare/36fcb5c1b74f...12f51a47897f **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d52b1f: Incremental refactoring to es6 classes and other f...
by GitHub 08 Jun '18

08 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d52b1f71bc106c3b402231d68c26a8bdb3575888 https://github.com/galaxyproject/galaxy/commit/d52b1f71bc106c3b402231d68c26… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Incremental refactoring to es6 classes and other fixes while tracking down workflow issue. Commit: bd248933f16ebab3af15e7e264ada3a89ff94337 https://github.com/galaxyproject/galaxy/commit/bd248933f16ebab3af15e7e264ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- More incremental refactoring while tracking down workflow bugs. Commit: 2de4219aae59cd93f7b9891d05d0d94859a9febc https://github.com/galaxyproject/galaxy/commit/2de4219aae59cd93f7b9891d05d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix a bunch of typos in workflow manager. Commit: 1f405d6916e2fdff808f9c65b5b3c5becedd21c9 https://github.com/galaxyproject/galaxy/commit/1f405d6916e2fdff808f9c65b5b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Drop unnecessary workflow enumerate in workflow manager. Commit: a4bf7aca6f5e556777d24d7d61dab31a0cc797e0 https://github.com/galaxyproject/galaxy/commit/a4bf7aca6f5e556777d24d7d61da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Minor refactoring in webapp to clarify history association logic (and maybe reuse it) Commit: 1fa77c38f611351bdc5bece9e9d06a16da08f42b https://github.com/galaxyproject/galaxy/commit/1fa77c38f611351bdc5bece9e9d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Respect workflow_building_modes.ENABLED in workflow manager's to_dict. Commit: d09dfca4292f9cf34ef1bad76c39eb21fe984518 https://github.com/galaxyproject/galaxy/commit/d09dfca4292f9cf34ef1bad76c39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- More typos, minor tweak to _associate_user_history Commit: b43ef5538121360c63b895d2a86dec91070598c0 https://github.com/galaxyproject/galaxy/commit/b43ef5538121360c63b895d2a86d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Drop unused edit_workflow_outputs functionality Commit: d2805bb6ca62dd690d1477adc676f1f62dd5577b https://github.com/galaxyproject/galaxy/commit/d2805bb6ca62dd690d1477adc676… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/utils/async-save-text.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/history.scss M client/package.json M client/yarn.lock M config/datatypes_conf.xml.sample M config/job_metrics_conf.xml.sample M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M config/plugins/visualizations/jqplot/jqplot_bar/static/script.css M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/base.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py A lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/permutations.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M run_tests.sh M scripts/grt/export.py M static/style/blue/base.css M templates/display_common.mako M templates/ind_share_base.mako R templates/sharing_base.mako M templates/webapps/galaxy/workflow/editor.mako M test/api/test_libraries.py M test/api/test_tools.py M test/base/data/rules_dsl_spec.yml M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh A test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into workflow_fixes Commit: 9a798395d13a061bf5355a88c154975da6a516cf https://github.com/galaxyproject/galaxy/commit/9a798395d13a061bf5355a88c154… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #6076 from dannon/workflow_fixes Workflow and remote-user related refactoring and a bug fix Compare: https://github.com/galaxyproject/galaxy/compare/db5dc5580c6e...9a798395d13a **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ed5645: add the canonical url to grt config
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: ed56454ca07f3e07ce2bfced8614ca3dc560649a https://github.com/galaxyproject/galaxy/commit/ed56454ca07f3e07ce2bfced8614… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M scripts/grt/grt.yml.sample Log Message: ----------- add the canonical url to grt config Commit: 36fcb5c1b74f7b7b84827311133957eb7249b277 https://github.com/galaxyproject/galaxy/commit/36fcb5c1b74f7b7b848273111339… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M scripts/grt/grt.yml.sample Log Message: ----------- Merge pull request #6301 from martenson/grt-config [18.05] add the canonical url to grt config Compare: https://github.com/galaxyproject/galaxy/compare/711070dc4c18...36fcb5c1b74f **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] cda465: Update Main
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cda4658c3726f5370d9e497f0b16f0fe60ae7218 https://github.com/galaxyproject/usegalaxy-playbook/commit/cda4658c3726f537… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 0701dc: Install plugin static content when full client bui...
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0701dcc565b5936d99d03337448a49b9eca6137e https://github.com/galaxyproject/usegalaxy-playbook/commit/0701dcc565b5936d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M env/common/client.yml M roles/usegalaxy_cvmfs/tasks/client.yml A roles/usegalaxy_cvmfs/tasks/client_plugins.yml M roles/usegalaxy_cvmfs/tasks/main.yml Log Message: ----------- Install plugin static content when full client build is not performed **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 703b5c: Install Bowtie2 2.3.4.2 and Diffbind 2.6.6.4 on Te...
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 703b5c1fd336456ac03643671dca27b2b9e8d5dc https://github.com/galaxyproject/usegalaxy-playbook/commit/703b5c1fd336456a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Install Bowtie2 2.3.4.2 and Diffbind 2.6.6.4 on Test and Main. Remove Diffbind 2.6.6.3 from Main **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 17d7c0: Consolidate use of get_repo_for_repository()
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17d7c0fb1f43a8cf377a76ea9484630d1c7be7f1 https://github.com/galaxyproject/galaxy/commit/17d7c0fb1f43a8cf377a76ea9484… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Consolidate use of get_repo_for_repository() Commit: a777c39b1eee65179bc1ae2e817ef269f22f2cd4 https://github.com/galaxyproject/galaxy/commit/a777c39b1eee65179bc1ae2e817e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Consolidate use of clone_repository() Commit: db5dc5580c6e62d98207cfef6db78929d5c02a88 https://github.com/galaxyproject/galaxy/commit/db5dc5580c6e62d98207cfef6db7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #6277 from nsoranzo/mercurial_api_removal2 Consolidate use of get_repo_for_repository() and clone_repository() Compare: https://github.com/galaxyproject/galaxy/compare/0dcca1a727cf...db5dc5580c6e **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 060d3f: Test list collection mapping over multidata input
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 060d3f0ffdefa9903d33847346a823acfdbaa969 https://github.com/galaxyproject/galaxy/commit/060d3f0ffdefa9903d33847346a8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Test list collection mapping over multidata input Commit: baa42fa8c6f867c6d2a1adcce9d8f3b946d10f0c https://github.com/galaxyproject/galaxy/commit/baa42fa8c6f867c6d2a1adcce9d8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix mapping list over multidata input Commit: 0dcca1a727cf3678386b319bd94d5421798e6eff https://github.com/galaxyproject/galaxy/commit/0dcca1a727cf3678386b319bd94d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6300 from mvdbeek/multidata_list_input Make simple lists selectable again in multidata inputs Compare: https://github.com/galaxyproject/galaxy/compare/e42e0c39a7d7...0dcca1a727cf **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy]
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/fix_workflow_link Home: https://github.com/galaxyproject/galaxy **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 671c4d: fix link to workflow list
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 671c4d4f5fad7d15e6b9f70d595cf9f14ec6aeda https://github.com/galaxyproject/galaxy/commit/671c4d4f5fad7d15e6b9f70d595c… Author: Björn Grüning <bjoern.gruening(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- fix link to workflow list Commit: e42e0c39a7d723ab9b99038b2d863c04848ff3e7 https://github.com/galaxyproject/galaxy/commit/e42e0c39a7d723ab9b99038b2d86… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6270 from galaxyproject/fix_workflow_link fix link to workflow list Compare: https://github.com/galaxyproject/galaxy/compare/eb6cefc514a0...e42e0c39a7d7 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 49a1be: Allow from_param to reference a child collection
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49a1be4f1de3cfe48bbfd0b709bc8a158f7d36e6 https://github.com/galaxyproject/galaxy/commit/49a1be4f1de3cfe48bbfd0b709bc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: bc8254faecf9b9f9bbd000d9ba7601ce9fe472a5 https://github.com/galaxyproject/galaxy/commit/bc8254faecf9b9f9bbd000d9ba76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b…. This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 3e22b0b11b600a4e957557d3cece03665bdc7de5 https://github.com/galaxyproject/galaxy/commit/3e22b0b11b600a4e957557d3cece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: 7b741a32cddb94442c7663f94c6c3b29e91e4158 https://github.com/galaxyproject/galaxy/commit/7b741a32cddb94442c7663f94c6c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Broken in commit 0ea8107191ea1a3bc8b4b57623c981c06f38092e . Reported by @lparsons in https://github.com/galaxyproject/galaxy/pull/6262#issuecomment-395113621 Commit: a2fe4b0c76fa9cfff9e974b76e4d5ea34679a881 https://github.com/galaxyproject/galaxy/commit/a2fe4b0c76fa9cfff9e974b76e4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge pull request #6295 from nsoranzo/release_18.01_followup_on_6262 [18.01] Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Commit: 3007c93d7c5bf6ccb7c6b8d5df95ebdf60ac4a8b https://github.com/galaxyproject/galaxy/commit/3007c93d7c5bf6ccb7c6b8d5df95… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6266 from jmchilton/from_param_fixes_backport [18.01] Backport fixes for collection output actions. Commit: 711070dc4c18af7a2da2a2a8bcafb4112efb0daf https://github.com/galaxyproject/galaxy/commit/711070dc4c18af7a2da2a2a8bcaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M run.sh M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: eb6cefc514a0ec96fbbb820e14712782653210c7 https://github.com/galaxyproject/galaxy/commit/eb6cefc514a0ec96fbbb820e1471… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/fae66e65f40b...eb6cefc514a0 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 49a1be: Allow from_param to reference a child collection
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 49a1be4f1de3cfe48bbfd0b709bc8a158f7d36e6 https://github.com/galaxyproject/galaxy/commit/49a1be4f1de3cfe48bbfd0b709bc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: bc8254faecf9b9f9bbd000d9ba7601ce9fe472a5 https://github.com/galaxyproject/galaxy/commit/bc8254faecf9b9f9bbd000d9ba76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b…. This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 3e22b0b11b600a4e957557d3cece03665bdc7de5 https://github.com/galaxyproject/galaxy/commit/3e22b0b11b600a4e957557d3cece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: 7b741a32cddb94442c7663f94c6c3b29e91e4158 https://github.com/galaxyproject/galaxy/commit/7b741a32cddb94442c7663f94c6c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Broken in commit 0ea8107191ea1a3bc8b4b57623c981c06f38092e . Reported by @lparsons in https://github.com/galaxyproject/galaxy/pull/6262#issuecomment-395113621 Commit: a2fe4b0c76fa9cfff9e974b76e4d5ea34679a881 https://github.com/galaxyproject/galaxy/commit/a2fe4b0c76fa9cfff9e974b76e4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge pull request #6295 from nsoranzo/release_18.01_followup_on_6262 [18.01] Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Commit: 3007c93d7c5bf6ccb7c6b8d5df95ebdf60ac4a8b https://github.com/galaxyproject/galaxy/commit/3007c93d7c5bf6ccb7c6b8d5df95… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6266 from jmchilton/from_param_fixes_backport [18.01] Backport fixes for collection output actions. Commit: 711070dc4c18af7a2da2a2a8bcafb4112efb0daf https://github.com/galaxyproject/galaxy/commit/711070dc4c18af7a2da2a2a8bcaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M run.sh M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/acb4cdf5843a...711070dc4c18 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f3dccb: Overhaul workflow execution response, including ap...
by GitHub 07 Jun '18

07 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3dccb7b6c897d44cb3fe94e6e4541f6273fe85c https://github.com/galaxyproject/galaxy/commit/f3dccb7b6c897d44cb3fe94e6e45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Overhaul workflow execution response, including appropriate text for new histories, and multiple executions. With links. Commit: 78fabab53c4e511dc5a3db4d3cc62eb71a5f097d https://github.com/galaxyproject/galaxy/commit/78fabab53c4e511dc5a3db4d3cc6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Drop debug statement Commit: 5845d64a48ad9528a45315cb2252afeaa067911b https://github.com/galaxyproject/galaxy/commit/5845d64a48ad9528a45315cb2252… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Cleanup in tool-form-composite Commit: 6c9953cfe2b98f0f23a4496d3a45437029b8945c https://github.com/galaxyproject/galaxy/commit/6c9953cfe2b98f0f23a4496d3a45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Clarify/reuse new history target logic, fix links to avoid redundant slash on root Commit: fae66e65f40b6d8c03fea1236e12a420fbb2058e https://github.com/galaxyproject/galaxy/commit/fae66e65f40b6d8c03fea1236e12… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #6240 from dannon/workflow_submit_text_links Workflow submit text links Compare: https://github.com/galaxyproject/galaxy/compare/ee56e570e027...fae66e65f40b **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 936c16: Index select2 field values
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 936c165818880bacd17416c7e848d6fba292e586 https://github.com/galaxyproject/galaxy/commit/936c165818880bacd17416c7e848… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Index select2 field values Commit: ee56e570e027eb7306becc95890c68fcb415c1fb https://github.com/galaxyproject/galaxy/commit/ee56e570e027eb7306becc95890c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #6286 from guerler/column_performance Index select2 field values Compare: https://github.com/galaxyproject/galaxy/compare/d2723428391a...ee56e570e027 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 49a1be: Allow from_param to reference a child collection
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 49a1be4f1de3cfe48bbfd0b709bc8a158f7d36e6 https://github.com/galaxyproject/galaxy/commit/49a1be4f1de3cfe48bbfd0b709bc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: bc8254faecf9b9f9bbd000d9ba7601ce9fe472a5 https://github.com/galaxyproject/galaxy/commit/bc8254faecf9b9f9bbd000d9ba76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b…. This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 3e22b0b11b600a4e957557d3cece03665bdc7de5 https://github.com/galaxyproject/galaxy/commit/3e22b0b11b600a4e957557d3cece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: 3007c93d7c5bf6ccb7c6b8d5df95ebdf60ac4a8b https://github.com/galaxyproject/galaxy/commit/3007c93d7c5bf6ccb7c6b8d5df95… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6266 from jmchilton/from_param_fixes_backport [18.01] Backport fixes for collection output actions. Compare: https://github.com/galaxyproject/galaxy/compare/a2fe4b0c76fa...3007c93d7c5b **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 031ce6: Fix delete "Collection Only" option in history men...
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 031ce67e996edc3c363bca1fbaf8572e92b5cbc7 https://github.com/galaxyproject/galaxy/commit/031ce67e996edc3c363bca1fbaf8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Fix delete "Collection Only" option in history menu. Broken with https://github.com/galaxyproject/galaxy/commit/7cc01380afd017c5cac2af2b2d73…. Commit: d2723428391a9355e5cd8bc34776d8bf589685a9 https://github.com/galaxyproject/galaxy/commit/d2723428391a9355e5cd8bc34776… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Merge pull request #6281 from jmchilton/fix_delete_collection_only_2 Fix delete "Collection Only" option in history menu. Compare: https://github.com/galaxyproject/galaxy/compare/97fd079255da...d2723428391a **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 644824: Remove todo
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 644824c499080648dcfce73693b1235b331c2def https://github.com/galaxyproject/galaxy/commit/644824c499080648dcfce73693b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Remove todo Commit: 8b31cb1b1a90bbc70c5efc352349cea0149a24bb https://github.com/galaxyproject/galaxy/commit/8b31cb1b1a90bbc70c5efc352349… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix help text for renaming operation in workflows Commit: 97fd079255dacbb085e89988d78a6f67cc99d342 https://github.com/galaxyproject/galaxy/commit/97fd079255dacbb085e89988d78a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #6274 from guerler/fix_help Fix help text for renaming operation in workflows Compare: https://github.com/galaxyproject/galaxy/compare/afa62a25e134...97fd079255da **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 7b741a: Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon`
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7b741a32cddb94442c7663f94c6c3b29e91e4158 https://github.com/galaxyproject/galaxy/commit/7b741a32cddb94442c7663f94c6c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Broken in commit 0ea8107191ea1a3bc8b4b57623c981c06f38092e . Reported by @lparsons in https://github.com/galaxyproject/galaxy/pull/6262#issuecomment-395113621 Commit: a2fe4b0c76fa9cfff9e974b76e4d5ea34679a881 https://github.com/galaxyproject/galaxy/commit/a2fe4b0c76fa9cfff9e974b76e4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge pull request #6295 from nsoranzo/release_18.01_followup_on_6262 [18.01] Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Compare: https://github.com/galaxyproject/galaxy/compare/a0004db7203e...a2fe4b0c76fa **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 502a0b: Set $XDG_DATA_HOME for fontconfig fonts, unset $FO...
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 502a0b338632c8ef8269497ca3c01dbcb54cba88 https://github.com/galaxyproject/usegalaxy-playbook/commit/502a0b338632c8ef… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Set $XDG_DATA_HOME for fontconfig fonts, unset $FONTCONFIG_FILE so that fonts.conf in conda envs will be used **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] e118cc: Main mutable configs for tool installs
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e118cc1a2487b918444819af42e015f19af75126 https://github.com/galaxyproject/usegalaxy-playbook/commit/e118cc1a2487b918… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable configs for tool installs **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 171251: Test mutable configs for new tool installs
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1712510e0e33aae6da05a8f802f9d7b001232254 https://github.com/galaxyproject/usegalaxy-playbook/commit/1712510e0e33aae6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs for new tool installs **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 1ab71f: Only update options if provided in parameter defin...
by GitHub 06 Jun '18

06 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ab71ff1901d9b3c231947171f4611f6e3dcbf56 https://github.com/galaxyproject/galaxy/commit/1ab71ff1901d9b3c231947171f46… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js Log Message: ----------- Only update options if provided in parameter definition Commit: afa62a25e1340f6ed9340a8b30e7ef53a9364262 https://github.com/galaxyproject/galaxy/commit/afa62a25e1340f6ed9340a8b30e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js Log Message: ----------- Merge pull request #6289 from guerler/fix_update_handler Only update options if provided in parameter definition Compare: https://github.com/galaxyproject/galaxy/compare/d95dcecbea34...afa62a25e134 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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