- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b31bd5: Extend PUT /api/workflows/{id} with additional wor...
by GitHub 31 Oct '16

31 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b31bd5be35b207ce3be3c287c5fa7831a40986d7 https://github.com/galaxyproject/galaxy/commit/b31bd5be35b207ce3be3c287c5fa… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Extend PUT /api/workflows/{id} with additional workflow properties Commit: aaf5b4d0f8a823d9b3d659b55f25ce207c47e25e https://github.com/galaxyproject/galaxy/commit/aaf5b4d0f8a823d9b3d659b55f25… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #3080 from tmcgowan/frequest_1842 Extend PUT /api/workflows/{id} with additional workflow properties Compare: https://github.com/galaxyproject/galaxy/compare/9e1331f1b37a...aaf5b4d0f8a8

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[galaxyproject/galaxy] b9e4bf: Sort bedtools output in bam_to_bigwig conversion
by GitHub 31 Oct '16

31 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b9e4bf58c5b656089ac8402632677503e6a86c65 https://github.com/galaxyproject/galaxy/commit/b9e4bf58c5b656089ac840263267… Author: Lance Parsons <lparsons(a)princeton.edu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- Sort bedtools output in bam_to_bigwig conversion Bedtools genomecov seems to output bedgraph files with chromosomes sorted in the order given in the chromInfo file. This can cause issues with bedGraphToBigWig which requires them sorted in a specific way. Fixes #2582. Commit: 9e1331f1b37a40d8894fc724bb745589bc5e213b https://github.com/galaxyproject/galaxy/commit/9e1331f1b37a40d8894fc724bb74… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- Merge pull request #3049 from lparsons/bam_to_bigwig Sort bedtools output in bam_to_bigwig conversion Compare: https://github.com/galaxyproject/galaxy/compare/25527bec32b2...9e1331f1b37a

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[galaxyproject/galaxy] d9dfc2: Move thumbnail list view to shared ui elements
by GitHub 31 Oct '16

31 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9dfc2cc78339f9b2158a07fff3df0a24d081865 https://github.com/galaxyproject/galaxy/commit/d9dfc2cc78339f9b2158a07fff3d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: A client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/client/app.css M config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/types.js A static/maps/mvc/ui/ui-thumbnails.js.map A static/scripts/mvc/ui/ui-thumbnails.js M static/style/blue/base.css Log Message: ----------- Move thumbnail list view to shared ui elements Commit: 296ef7e232468a2311ba18763752d97e10c63a2d https://github.com/galaxyproject/galaxy/commit/296ef7e232468a2311ba18763752… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M static/maps/mvc/ui/ui-tabs.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/ui/ui-tabs.js Log Message: ----------- Hide tabs navigation if there is only one tab Commit: aab59be19160a97f41c60b7dab741825c90be934 https://github.com/galaxyproject/galaxy/commit/aab59be19160a97f41c60b7dab74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix margin Commit: ec9ca3ffd1bcb2a6e70a5a1f2c8e0183e80ddc1a https://github.com/galaxyproject/galaxy/commit/ec9ca3ffd1bcb2a6e70a5a1f2c8e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M config/plugins/visualizations/charts/static/client/views/editor.js M static/maps/mvc/ui/ui-thumbnails.js.map M static/scripts/mvc/ui/ui-thumbnails.js Log Message: ----------- Fix list view title Commit: 0b1c171ebc2b9b0605a6ef1e8e5b68e20d579c74 https://github.com/galaxyproject/galaxy/commit/0b1c171ebc2b9b0605a6ef1e8e5b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M config/plugins/visualizations/charts/static/client/views/editor.js M static/maps/mvc/ui/ui-tabs.js.map M static/maps/mvc/ui/ui-thumbnails.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/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M test/qunit/tests/ui_tests.js Log Message: ----------- Revise tab viewer, add test cases Commit: c4526bdaba29ccc9b045dea429dbc0c3fa0e5b15 https://github.com/galaxyproject/galaxy/commit/c4526bdaba29ccc9b045dea429db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M static/maps/mvc/ui/ui-tabs.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/ui/ui-tabs.js Log Message: ----------- Hide tab navbar if there is only one tab available Commit: 25527bec32b2431f1a8769ef79f34ad9af38c0db https://github.com/galaxyproject/galaxy/commit/25527bec32b2431f1a8769ef79f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js A client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/client/app.css M config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/types.js M static/maps/mvc/ui/ui-tabs.js.map A static/maps/mvc/ui/ui-thumbnails.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/ui/ui-tabs.js A static/scripts/mvc/ui/ui-thumbnails.js M static/style/blue/base.css M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #3079 from guerler/reusable_grid_view Move thumbnail list view to shared ui elements, revise tabs, add test cases Compare: https://github.com/galaxyproject/galaxy/compare/f9ee0f86376f...25527bec32b2

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[galaxyproject/galaxy] 4bfac4: Fix flake8 errors and Python3 compatibility for do...
by GitHub 31 Oct '16

31 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4bfac4536971c54a704c76de083de0600332442c https://github.com/galaxyproject/galaxy/commit/4bfac4536971c54a704c76de083d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M doc/patch.py Log Message: ----------- Fix flake8 errors and Python3 compatibility for doc/patch.py Commit: a21ed34efb695fb71f1c7616dc1655de8b54be41 https://github.com/galaxyproject/galaxy/commit/a21ed34efb695fb71f1c7616dc16… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: R doc/source/admin/interactive_environments_success.png A doc/source/dev/interactive_environments_success.png Log Message: ----------- Move png in the right directory Broken in #2543. Commit: 8a17143bc77ce370974e35f51d699f8029edd647 https://github.com/galaxyproject/galaxy/commit/8a17143bc77ce370974e35f51d69… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: R doc/source/lib/galaxy.util.backports.importlib.rst R scripts/bootstrap_history_announce_template.rst Log Message: ----------- Remove unused files Commit: e6d0b69ec89786f56fa71d2e893b2361bbe55d0e https://github.com/galaxyproject/galaxy/commit/e6d0b69ec89786f56fa71d2e893b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M doc/source/dev/build_a_job_runner.rst A doc/source/dev/inherit.png A doc/source/dev/queue.png A doc/source/dev/queue_b.png A doc/source/dev/runner_diag.png Log Message: ----------- Add and use local images for build runner doc Commit: 3180b631662ced589fe9db42d27caa58638b5f8d https://github.com/galaxyproject/galaxy/commit/3180b631662ced589fe9db42d27c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M .gitignore M Makefile M doc/Makefile M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/dev/index.rst M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Properly integrate tool XML schema with docs Generate intermediate rst file instead of html Move generation to doc/Makefile Use pandoc to generate table of contents and fragment ids. Remove nested inline markup (not supported by reStructuredText) Fix https and other links. Commit: 527e332aa39e82224965e6aaef94ffaa1cf956bf https://github.com/galaxyproject/galaxy/commit/527e332aa39e82224965e6aaef94… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-24 (Mon, 24 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/mulled_containers.rst M doc/source/conf.py M doc/source/index.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.linters.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/managers/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/simplegraph.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/bootstrap_history.py M scripts/galaxy-main Log Message: ----------- Fix a bunch of errors reported by Sphinx Commit: f9ee0f86376f90ede636e4874cca120d30e7cd8c https://github.com/galaxyproject/galaxy/commit/f9ee0f86376f90ede636e4874cca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M Makefile M doc/Makefile M doc/parse_gx_xsd.py M doc/patch.py M doc/schema_template.md M doc/source/admin/conda_faq.rst M doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments_success.png M doc/source/admin/mulled_containers.rst M doc/source/conf.py M doc/source/dev/build_a_job_runner.rst M doc/source/dev/index.rst A doc/source/dev/inherit.png A doc/source/dev/interactive_environments_success.png A doc/source/dev/queue.png A doc/source/dev/queue_b.png A doc/source/dev/runner_diag.png M doc/source/index.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.linters.rst M doc/source/lib/galaxy.tools.parameters.rst R doc/source/lib/galaxy.util.backports.importlib.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/managers/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/simplegraph.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/bootstrap_history.py R scripts/bootstrap_history_announce_template.rst M scripts/galaxy-main Log Message: ----------- Merge pull request #3086 from nsoranzo/fix_doc Properly integrate tool XML schema with docs Compare: https://github.com/galaxyproject/galaxy/compare/f0c5d5ca39d1...f9ee0f86376f

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[galaxyproject/galaxy] 10ce53: Fix qunit local testing install -- now runs on mod...
by GitHub 31 Oct '16

31 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10ce532c15a5ab7373f40a1452f3e1ed236d3ec7 https://github.com/galaxyproject/galaxy/commit/10ce532c15a5ab7373f40a1452f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M test/qunit/package.json Log Message: ----------- Fix qunit local testing install -- now runs on modern node (v6.9.1) with no system packages, just 'npm install', 'grunt'. Commit: f0c5d5ca39d1e7456aea0d81fdcba345ce28a868 https://github.com/galaxyproject/galaxy/commit/f0c5d5ca39d1e7456aea0d81fdcb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M test/qunit/package.json Log Message: ----------- Merge pull request #3089 from dannon/fix_local_qunit Fix qunit local testing install -- now runs on modern node (v6.9.1) w… Compare: https://github.com/galaxyproject/galaxy/compare/29b07cbb2a5a...f0c5d5ca39d1

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[galaxyproject/galaxy] 19b568: Fix XSD for exclude_min and exclude_max attributes...
by GitHub 31 Oct '16

31 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19b568cb9310b03b0cc74d3e6a7745b83074a0b8 https://github.com/galaxyproject/galaxy/commit/19b568cb9310b03b0cc74d3e6a77… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix XSD for exclude_min and exclude_max attributes of tool param validator Commit: 29b07cbb2a5aa05eb3636dcd9c3f0e15c42d21a1 https://github.com/galaxyproject/galaxy/commit/29b07cbb2a5aa05eb3636dcd9c3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3108 from gregvonkuster/xsd Fix XSD for exclude_min and exclude_max Compare: https://github.com/galaxyproject/galaxy/compare/a1e5118050ee...29b07cbb2a5a

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[galaxyproject/galaxy] 838e2c: Add routes to get genomes indexes and sequences
by GitHub 31 Oct '16

31 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 838e2cbb66f2d7138eed51e434e623f057625042 https://github.com/galaxyproject/galaxy/commit/838e2cbb66f2d7138eed51e434e6… Author: Jim Johnson <jj(a)umn.edu> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add routes to get genomes indexes and sequences So igv.js can retrieve genome data Commit: a1e5118050ee5cf827396e2b2b38f147c51ed772 https://github.com/galaxyproject/galaxy/commit/a1e5118050ee5cf827396e2b2b38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3109 from jj-umn/patch-5 Add routes to get genomes indexes and sequences Compare: https://github.com/galaxyproject/galaxy/compare/c626ff8b2eff...a1e5118050ee

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[galaxyproject/galaxy] ac9d21: Eagerload tags and annotations in history display
by GitHub 29 Oct '16

29 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac9d21d510320de98d7db87fd97e1246d468728a https://github.com/galaxyproject/galaxy/commit/ac9d21d510320de98d7db87fd97e… Author: James Taylor <james(a)jamestaylor.org> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Eagerload tags and annotations in history display Commit: c626ff8b2effa390de4816eafe507ea5b1fd1d6b https://github.com/galaxyproject/galaxy/commit/c626ff8b2effa390de4816eafe50… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #3110 from jxtx/dev Eagerload tags and annotations in history display Compare: https://github.com/galaxyproject/galaxy/compare/2458c5455fe0...c626ff8b2eff

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[galaxyproject/usegalaxy-playbook] 6be703: Update Test
by GitHub 28 Oct '16

28 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6be70382ba086a0cde9a92594ed7b8b5276727f7 https://github.com/galaxyproject/usegalaxy-playbook/commit/6be70382ba086a0c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M stage/galaxy_version.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] 6e4f3d: Revert menu.js, tool-form.js to pre-webhooks-PR
by GitHub 27 Oct '16

27 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e4f3d9d2d1a01b539d412aad5bb8fbe0ba95a17 https://github.com/galaxyproject/galaxy/commit/6e4f3d9d2d1a01b539d412aad5bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.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/layout/menu.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Revert menu.js, tool-form.js to pre-webhooks-PR Commit: 62773a72c728b8bab46804d2128e46f62d45cd1d https://github.com/galaxyproject/galaxy/commit/62773a72c728b8bab46804d2128e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js 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 Log Message: ----------- Reapply isolated menu.js webhook changes Commit: 67b1d45e3657af077005ed7b0b1469a7fd3f42d0 https://github.com/galaxyproject/galaxy/commit/67b1d45e3657af077005ed7b0b14… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form.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.js Log Message: ----------- Reapply isolated tool-form.js webhook changes Commit: 2458c5455fe07c7832cb30fd5bdedc9770db6f42 https://github.com/galaxyproject/galaxy/commit/2458c5455fe07c7832cb30fd5bde… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.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.js Log Message: ----------- Merge pull request #3102 from dannon/fix_webhook_js_merge Fixes for remaining webhooks PR issues. Compare: https://github.com/galaxyproject/galaxy/compare/660d70f8b4da...2458c5455fe0

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[galaxyproject/galaxy] 83a294: Lint fixes to workflow controller
by GitHub 27 Oct '16

27 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83a29454caea72915386c58a7188e08cd4597d35 https://github.com/galaxyproject/galaxy/commit/83a29454caea72915386c58a7188… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Lint fixes to workflow controller Commit: 660d70f8b4da32f5ebd5981ad9eb27e87a79da73 https://github.com/galaxyproject/galaxy/commit/660d70f8b4da32f5ebd5981ad9eb… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #3103 from dannon/minor_style_fixes Lint fixes to workflow controller Compare: https://github.com/galaxyproject/galaxy/compare/0eff2ec6479b...660d70f8b4da

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[galaxyproject/galaxy] 1288cf: Add workflow save-as functionality. Issue 3000
by GitHub 27 Oct '16

27 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1288cf0505eea6139bf9f34d60e6b255268d717d https://github.com/galaxyproject/galaxy/commit/1288cf0505eea6139bf9f34d60e6… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-view.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-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Add workflow save-as functionality. Issue 3000 Commit: 2ab0b18706dc54cde3507e194a935f513c68119c https://github.com/galaxyproject/galaxy/commit/2ab0b18706dc54cde3507e194a93… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Allow names with spaces Commit: 38464b5b284289c66263adc19afa0a6be2e24389 https://github.com/galaxyproject/galaxy/commit/38464b5b284289c66263adc19afa… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Originating workflow must be unchanged, load save as workflow to editor on save. Commit: 0eff2ec6479b321d9fc653aa9eaf79559fc50e56 https://github.com/galaxyproject/galaxy/commit/0eff2ec6479b321d9fc653aa9eaf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge remote-tracking branch 'tmcgowan/issue_3000' into dev Compare: https://github.com/galaxyproject/galaxy/compare/541643d7fe28...0eff2ec6479b

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[galaxyproject/infrastructure-playbook] 9db378: Increase upstream proxy timeout for galaxy install...
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9db37851eff6bc685efa1be40b6601a5257ca2ed https://github.com/galaxyproject/infrastructure-playbook/commit/9db37851eff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M taccenv/host_vars/galaxy04.tacc.utexas.edu.yml Log Message: ----------- Increase upstream proxy timeout for galaxy installers

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[galaxyproject/galaxy] 69636f: Add CEL file as a datatype
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69636f5e65e6b3ad2c8d7e3c300cd81418bb6206 https://github.com/galaxyproject/galaxy/commit/69636f5e65e6b3ad2c8d7e3c300c… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add CEL file as a datatype Commit: 7e2725d1250fef33d1d03cc4e15b29de6f1a540f https://github.com/galaxyproject/galaxy/commit/7e2725d1250fef33d1d03cc4e15b… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add CEL datatypes to datatypes conf sample Commit: f891034390908bd6a374bf140a57ac76afefefd9 https://github.com/galaxyproject/galaxy/commit/f891034390908bd6a374bf140a57… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Lowercase the datatypes, add edam_data, thanks @nsoranzo Commit: a6f1783b366293a0d87ee941882e449f092cce95 https://github.com/galaxyproject/galaxy/commit/a6f1783b366293a0d87ee941882e… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: A lib/galaxy/datatypes/test/test.CEL Log Message: ----------- Small test case CEL datatype, v4 Commit: 827e61a98cdfb3074d49df25b3ac0b30ce32d0bc https://github.com/galaxyproject/galaxy/commit/827e61a98cdfb3074d49df25b3ac… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add doctests Commit: 5c1d0982e33e3c5464bb6374d33ed9a7bb76a648 https://github.com/galaxyproject/galaxy/commit/5c1d0982e33e3c5464bb6374d33e… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- lint issues Commit: 541643d7fe28abeac4a69147aa3ae30f84d438ae https://github.com/galaxyproject/galaxy/commit/541643d7fe28abeac4a69147aa3a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.CEL Log Message: ----------- Merge pull request #3073 from nturaga/add_cel_datatype Add CEL datatype Compare: https://github.com/galaxyproject/galaxy/compare/f21279d473fa...541643d7fe28

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[galaxyproject/usegalaxy-playbook] 1d8cc9: Fix admin users
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1d8cc9c82c9ed83814d8b5d46780634e29a70571 https://github.com/galaxyproject/usegalaxy-playbook/commit/1d8cc9c82c9ed838… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M production/secret_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Fix admin users

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[galaxyproject/galaxy] 2ec9c0: Log loading of resources from *.loc files
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ec9c05380356ba543b29bae44cc3bdd947196a2 https://github.com/galaxyproject/galaxy/commit/2ec9c05380356ba543b29bae44cc… Author: Peter Cock <p.j.a.cock(a)googlemail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Log loading of resources from *.loc files Example output: ``` $ grep "lines from" paster.log galaxy.tools.data DEBUG 2016-10-26 10:24:22,742 Loaded 0 lines from 'tool-data/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2016-10-26 10:24:22,753 Loaded 0 lines from 'tool-data/bfast_indexes.loc' for 'bfast_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,848 Loaded 24 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2016-10-26 10:24:22,859 Loaded 0 lines from 'tool-data/maf_index.loc' for 'indexed_maf_files' galaxy.tools.data DEBUG 2016-10-26 10:24:22,865 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2016-10-26 10:24:22,878 Loaded 0 lines from 'tool-data/perm_base_index.loc' for 'perm_base_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,890 Loaded 0 lines from 'tool-data/perm_color_index.loc' for 'perm_color_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,895 Loaded 0 lines from 'tool-data/picard_index.loc' for 'picard_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,899 Loaded 0 lines from 'tool-data/picard_index.loc' for 'srma_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,937 Loaded 0 lines from 'tool-data/mosaik_index.loc' for 'mosaik_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,943 Loaded 0 lines from 'tool-data/twobit.loc' for 'twobit' ... galaxy.tools.data DEBUG 2016-10-26 10:24:24,036 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2016-10-26 10:24:24,106 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2016-10-26 10:24:24,112 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_d.loc' for 'blastdb_d' ``` Commit: f21279d473fa8f19d3881af35d3066e79d757304 https://github.com/galaxyproject/galaxy/commit/f21279d473fa8f19d3881af35d30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #3099 from peterjc/patch-5 Log loading of resources from *.loc files Compare: https://github.com/galaxyproject/galaxy/compare/90d143cda16d...f21279d473fa

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[galaxyproject/galaxy] fc0271: Fix BLAST database *.loc files inconsistency
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fc027124e73ee391e4b4045b2abc68fd942f910c https://github.com/galaxyproject/galaxy/commit/fc027124e73ee391e4b4045b2abc… Author: Peter Cock <p.j.a.cock(a)googlemail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Fix BLAST database *.loc files inconsistency We should have all of the ``blast*.loc`` files in the sample configuration, or none of them. Historically Galaxy included only the nucleotide BLAST database ``blastdb.loc`` file for use with mega-blast, with ``blastdb_p.loc`` later for protein databases added as part of the BLAST+ suite (which initially was in the main Galaxy repository). In a3018feb028658fc3a7071803b7b49cb575e7358 the mega-blast tool was moved to the Tool Shed, and the ``blastdb.loc`` entry removed. Likewise the BLAST+ tools were moved to the Tool Shed, but the ``blastdb_p.loc`` entry remains. Later (on the Tool Shed only?) ``blastdb_d.loc``was added for protein domain databases. Commit: 90d143cda16d7c7a0938e255c08bf9db7fea727c https://github.com/galaxyproject/galaxy/commit/90d143cda16d7c7a0938e255c08b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Merge pull request #3098 from peterjc/patch-6 Fix BLAST database *.loc files inconsistency Compare: https://github.com/galaxyproject/galaxy/compare/ab42b7b15c50...90d143cda16d

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[galaxyproject/galaxy] ca8cd5: Avoid pointless lambda function
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca8cd524a1f882b7de2aaf5f56d8b2878c07739a https://github.com/galaxyproject/galaxy/commit/ca8cd524a1f882b7de2aaf5f56d8… Author: Peter Cock <p.j.a.cock(a)googlemail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Avoid pointless lambda function The lambda function used a ternary if/else anyway, just do this directly - its shorter and clearer. Commit: ab42b7b15c50c7ae4a4a582ebc1df2780e1538de https://github.com/galaxyproject/galaxy/commit/ab42b7b15c50c7ae4a4a582ebc1d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #3097 from peterjc/patch-4 Avoid pointless lambda function Compare: https://github.com/galaxyproject/galaxy/compare/35346fdb3e67...ab42b7b15c50

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[galaxyproject/galaxy] 17da51: Include filenames in loc file DEBUG lines
by GitHub 26 Oct '16

26 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17da51abdc61e9fb1e3f76b36316c9dbf3c836e6 https://github.com/galaxyproject/galaxy/commit/17da51abdc61e9fb1e3f76b36316… Author: Peter Cock <p.j.a.cock(a)googlemail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Include filenames in loc file DEBUG lines This will help debugging where multiple (possibly conflicting) ``*.loc`` files come from, e.g. ``` galaxy.tools.data DEBUG 2016-10-25 18:34:50,841 Loaded tool data table 'blastdb_p' galaxy.tools.data DEBUG 2016-10-25 18:34:51,356 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2016-10-25 18:34:51,359 Loading another instance of data table 'blastdb_p', attempting to merge content. galaxy.tools.data DEBUG 2016-10-25 18:34:51,375 Loaded tool data table 'blastdb_d' ``` Evidently I may have at least two copies of ``blastdb_p.loc``, but where are they? Commit: 35346fdb3e6764b14ae3359fb9ea31c03d932ea0 https://github.com/galaxyproject/galaxy/commit/35346fdb3e6764b14ae3359fb9ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #3095 from peterjc/patch-4 Include filenames in loc file DEBUG lines Compare: https://github.com/galaxyproject/galaxy/compare/8da4ad6563f2...35346fdb3e67

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[galaxyproject/usegalaxy-playbook] 860a2d: Increase htseq-count memory to 16GB
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 860a2d104193a693a5f8f224c29a14df956d13d3 https://github.com/galaxyproject/usegalaxy-playbook/commit/860a2d104193a693… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase htseq-count memory to 16GB

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[galaxyproject/usegalaxy-playbook] 48e2dd: Updated integrated_tool_panel.xml from Main
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 48e2ddcc7436782a270393ded55859f00b4bd24f https://github.com/galaxyproject/usegalaxy-playbook/commit/48e2ddcc7436782a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- Updated integrated_tool_panel.xml from Main Commit: c346c541753039291d17459f1b9ab9886bee41b8 https://github.com/galaxyproject/usegalaxy-playbook/commit/c346c54175303929… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M production/secret_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Update Test/Main admin users Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/fe578b76e94d...…

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[galaxyproject/galaxy] 575373: Remove run_complete.mako -- unused and cruft from ...
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 575373c8f304967b224af128774ad646a40cde3b https://github.com/galaxyproject/galaxy/commit/575373c8f304967b224af128774a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-23 (Sun, 23 Oct 2016) Changed paths: R templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- Remove run_complete.mako -- unused and cruft from merge chaos in webhooks PR. Commit: d2ff7345a8c0fbdb8c5d88e86e428f79c263d462 https://github.com/galaxyproject/galaxy/commit/d2ff7345a8c0fbdb8c5d88e86e42… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: R templates/webapps/galaxy/workflow/index.mako R templates/webapps/galaxy/workflow/missing_tools.mako R templates/webapps/galaxy/workflow/myexp_export_content.mako R templates/webapps/galaxy/workflow/rename.mako Log Message: ----------- Remove 4 additional mako files per nsoranzo Commit: 8da4ad6563f2d37309494aa86e1f8ed2595a6af9 https://github.com/galaxyproject/galaxy/commit/8da4ad6563f2d37309494aa86e1f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: R templates/webapps/galaxy/workflow/index.mako R templates/webapps/galaxy/workflow/missing_tools.mako R templates/webapps/galaxy/workflow/myexp_export_content.mako R templates/webapps/galaxy/workflow/rename.mako R templates/webapps/galaxy/workflow/run_complete.mako Log Message: ----------- Merge pull request #3082 from dannon/remove_run_complete Remove run_complete.mako -- unused and cruft from merge chaos in webh… Compare: https://github.com/galaxyproject/galaxy/compare/62c77e2cc457...8da4ad6563f2

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[galaxyproject/galaxy] ae0d0a: Update the schema to be correct and recent
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ae0d0a23e273d39f64da2550da34adee9a540bb2 https://github.com/galaxyproject/galaxy/commit/ae0d0a23e273d39f64da2550da34… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M doc/source/slideshow/architecture/images/galaxy_schema.png Log Message: ----------- Update the schema to be correct and recent Commit: 62c77e2cc457a5cb2f33b7d75e247ecf13ba57d8 https://github.com/galaxyproject/galaxy/commit/62c77e2cc457a5cb2f33b7d75e24… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M doc/source/slideshow/architecture/images/galaxy_schema.png Log Message: ----------- Merge pull request #3091 from dannon/update_old_schema Update the schema image in architecture slides to be correct and recent (and use git-lfs for doc pngs) Compare: https://github.com/galaxyproject/galaxy/compare/9d402eaf1ab1...62c77e2cc457

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[galaxyproject/galaxy] a431d8: Add tool xml reload to tool run page - for admins ...
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a431d88293faf8f6286cae416f8842ce186692c4 https://github.com/galaxyproject/galaxy/commit/a431d88293faf8f6286cae416f88… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-18 (Tue, 18 Oct 2016) 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: ----------- Add tool xml reload to tool run page - for admins only Commit: f9357ea07ddf0525b3a82021c9e11f690c700d67 https://github.com/galaxyproject/galaxy/commit/f9357ea07ddf0525b3a82021c9e1… Author: tmcgowan <mcgo0092(a)umn.edu> Date: 2016-10-20 (Thu, 20 Oct 2016) 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: ----------- Add modal confirmation for tool reload. Commit: 9d402eaf1ab13b03894a27645368f12a9d42289c https://github.com/galaxyproject/galaxy/commit/9d402eaf1ab13b03894a27645368… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) 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 remote-tracking branch 'tmcgowan/frequest_943' into dev Compare: https://github.com/galaxyproject/galaxy/compare/05be84ba47c0...9d402eaf1ab1

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[galaxyproject/usegalaxy-playbook] fe578b: Add a manual dependency path to Main for SRA Tools...
by GitHub 25 Oct '16

25 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fe578b76e94d3078ec07a6d187f88038d0f6730e https://github.com/galaxyproject/usegalaxy-playbook/commit/fe578b76e94d3078… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Add a manual dependency path to Main for SRA Tools to find ascp.

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