- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6bef1f: remove an extra F from the folder ID
by GitHub 17 Jan '18

17 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 6bef1fcbaa1df5690658f7b14512d212c115a0e5 https://github.com/galaxyproject/galaxy/commit/6bef1fcbaa1df5690658f7b14512… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- remove an extra F from the folder ID Commit: c3d145ce995e9e5f8e54dd7e81333bcc712bf4ab https://github.com/galaxyproject/galaxy/commit/c3d145ce995e9e5f8e54dd7e8133… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M templates/webapps/galaxy/history/display_structured.mako Log Message: ----------- Merge pull request #5327 from martenson/fix-structured-lib-link [17.09] fix link to library from history structure view Compare: https://github.com/galaxyproject/galaxy/compare/a6e9504dde8b...c3d145ce995e

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[galaxyproject/galaxy] be4fba: Add option to replace failed elements on job rerun
by GitHub 17 Jan '18

17 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be4fba3566ac70306451d84b069adc462baeb73c https://github.com/galaxyproject/galaxy/commit/be4fba3566ac70306451d84b069a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Add option to replace failed elements on job rerun Replacing failed collection elements was already possible when dependent jobs were found (https://github.com/galaxyproject/galaxy/pull/5247) This commit restructures the remapping so that remapping is possible when no dependent jobs are available. This also simplifies the replacement of HDAs between old and new jobs. Commit: bf2c9bab344c7acd9a1140c07037c51d91016914 https://github.com/galaxyproject/galaxy/commit/bf2c9bab344c7acd9a1140c07037… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #5321 from mvdbeek/rerun_without_dependent_jobs Add option to replace failed elements on job rerun Compare: https://github.com/galaxyproject/galaxy/compare/d2530f4f2412...bf2c9bab344c

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[galaxyproject/galaxy] 4b2bf1: fix for microbial import tool
by GitHub 17 Jan '18

17 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b2bf122b627d4dfbd87e9491cbf97755f40a9bf https://github.com/galaxyproject/galaxy/commit/4b2bf122b627d4dfbd87e9491cbf… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M tools/data_source/microbial_import_code.py Log Message: ----------- fix for microbial import tool There seems to be no UnvalidatedValue class anymore. So I removed these checks which seems to make the tool functional again. Note that there is one more instance of such a check in the Galaxy sources (in tools/parameters/basic.py). I guess this can also be removed? Commit: b59fb06fd92f71211bf473f30e8d0341fb4650b4 https://github.com/galaxyproject/galaxy/commit/b59fb06fd92f71211bf473f30e8d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M tools/data_source/microbial_import_code.py Log Message: ----------- Remove unused import Commit: d2530f4f2412e48b3394b5f52327416b93c895aa https://github.com/galaxyproject/galaxy/commit/d2530f4f2412e48b3394b5f52327… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M tools/data_source/microbial_import_code.py Log Message: ----------- Merge pull request #5258 from bernt-matthias/topic/getmicrobedata-quick-fix Topic/getmicrobedata quick fix Compare: https://github.com/galaxyproject/galaxy/compare/3cc4760727a1...d2530f4f2412

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[galaxyproject/galaxy] e63f8c: Uninstall a tool by default (vs. deactivating it)
by GitHub 17 Jan '18

17 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e63f8c8a26b23bec5136cf19877a1f32ed9f4f5d https://github.com/galaxyproject/galaxy/commit/e63f8c8a26b23bec5136cf19877a… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Uninstall a tool by default (vs. deactivating it) Commit: e5de36e3c500ab2c7d3abcdfff8b405d80dd8536 https://github.com/galaxyproject/galaxy/commit/e5de36e3c500ab2c7d3abcdfff8b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- use Python bool as argument Commit: 878c68e2a201905bb40901e66af0c701ebe30eea https://github.com/galaxyproject/galaxy/commit/878c68e2a201905bb40901e66af0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- set the default after the form submission action to not override Commit: 3cc4760727a127f5d936d9c47165a8ec90db730d https://github.com/galaxyproject/galaxy/commit/3cc4760727a127f5d936d9c47165… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Merge pull request #5300 from afgane/dev Uninstall a tool by default (vs. deactivating it) Compare: https://github.com/galaxyproject/galaxy/compare/b91d8e139817...3cc4760727a1

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[galaxyproject/usegalaxy-playbook] 4480e3: Re-enable sentry on test
by GitHub 17 Jan '18

17 Jan '18

Branch: refs/heads/test_reenable_sentry Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4480e3199496563ddcf31c1aa2e88a5031700fc5 https://github.com/galaxyproject/usegalaxy-playbook/commit/4480e3199496563d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Re-enable sentry on test

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[galaxyproject/galaxy] 8b76a5: Added support for recursively discovering output d...
by GitHub 17 Jan '18

17 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b76a5a698fd3bc13d4acc38194221def9ed5163 https://github.com/galaxyproject/galaxy/commit/8b76a5a698fd3bc13d4acc381942… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-12-21 (Thu, 21 Dec 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_collection_def.py A test/functional/tools/multi_output_recurse.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Added support for recursively discovering output datasets Commit: 3c7248a0884588826a4b5cc8fb699ad0e042d7ce https://github.com/galaxyproject/galaxy/commit/3c7248a0884588826a4b5cc8fb69… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-12-21 (Thu, 21 Dec 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Added schema entry for discover_datasets recurse attribute Commit: bae64800f072f84c7bbfda2c29f4330d6ca6552e https://github.com/galaxyproject/galaxy/commit/bae64800f072f84c7bbfda2c29f4… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix discover_target_directory and pass correct parameter Fix according to review comment: https://github.com/galaxyproject/galaxy/pull/5240/files#r159138549 Commit: b91d8e1398174d3ee530c0ed95a31c752423e023 https://github.com/galaxyproject/galaxy/commit/b91d8e1398174d3ee530c0ed95a3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/multi_output_recurse.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #5240 from gvlproject/discover_datasets_recursive Added support for recursively discovering output datasets Compare: https://github.com/galaxyproject/galaxy/compare/542a489079bc...b91d8e139817

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[galaxyproject/galaxy] a5cef0: Fixes the --no-client-build startup option (and re...
by GitHub 17 Jan '18

17 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a5cef0fe681552df6876ef88bdc46ce0b7e36e6a https://github.com/galaxyproject/galaxy/commit/a5cef0fe681552df6876ef88bdc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M scripts/common_startup.sh M scripts/common_startup_functions.sh Log Message: ----------- Fixes the --no-client-build startup option (and renames it --skip-client-build, too) Commit: 542a489079bcbc426dd957e43b44e56f94a1bfaa https://github.com/galaxyproject/galaxy/commit/542a489079bcbc426dd957e43b44… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M scripts/common_startup.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #5294 from dannon/fix_skip_client_build Fixes the --no-client-build startup option Compare: https://github.com/galaxyproject/galaxy/compare/5b60d0be27d3...542a489079bc

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[galaxyproject/infrastructure-playbook] 297484: Set up nn14 as a liteenv host
by GitHub 16 Jan '18

16 Jan '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 297484ca90d5540a9871729320571f443c011a45 https://github.com/galaxyproject/infrastructure-playbook/commit/297484ca90d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-16 (Tue, 16 Jan 2018) Changed paths: M env/galaxy/inventory M roles/nfs/tasks/main.yml Log Message: ----------- Set up nn14 as a liteenv host

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[galaxyproject/galaxy] 69e35a: allow message to be modified on ldda
by GitHub 15 Jan '18

15 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69e35a24345469f1bbb4da46a4bfd3b8786e5ece https://github.com/galaxyproject/galaxy/commit/69e35a24345469f1bbb4da46a4bf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/managers/library_datasets.py Log Message: ----------- allow message to be modified on ldda implements #5309 Commit: 5b60d0be27d3ff24b5aec55e45e354944190fc7a https://github.com/galaxyproject/galaxy/commit/5b60d0be27d3ff24b5aec55e45e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/managers/library_datasets.py Log Message: ----------- Merge pull request #5312 from martenson/libraries-implement-message allow message to be modified on ldda Compare: https://github.com/galaxyproject/galaxy/compare/02ff53571a5b...5b60d0be27d3

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[galaxyproject/galaxy] e7b98d: Fix string substitution syntax
by GitHub 15 Jan '18

15 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e7b98dff47d2ae48c1d1cc9a609d7de992f23ac2 https://github.com/galaxyproject/galaxy/commit/e7b98dff47d2ae48c1d1cc9a609d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix string substitution syntax Commit: 02ff53571a5b7682a1fa74c8bd867c0233593954 https://github.com/galaxyproject/galaxy/commit/02ff53571a5b7682a1fa74c8bd86… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #5311 from mvdbeek/fix_sort_order_tool Fix string substitution syntax in sort tool action Compare: https://github.com/galaxyproject/galaxy/compare/9ac5052d7acf...02ff53571a5b

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[galaxyproject/galaxy] 6cb9d6: Fix Galaxy instance startup error
by GitHub 14 Jan '18

14 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6cb9d664dee2af178f179e9fc3f528710c5d4507 https://github.com/galaxyproject/galaxy/commit/6cb9d664dee2af178f179e9fc3f5… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-14 (Sun, 14 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Fix Galaxy instance startup error Commit: 9ac5052d7acfd0099ecfafd7109bb30b6a1e5145 https://github.com/galaxyproject/galaxy/commit/9ac5052d7acfd0099ecfafd7109b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-01-14 (Sun, 14 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5306 from bgruening/structure_view_history Fix Galaxy instance startup error Compare: https://github.com/galaxyproject/galaxy/compare/199457f23bf6...9ac5052d7acf

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[galaxyproject/galaxy] a847db: Fix tool report submission
by GitHub 12 Jan '18

12 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: a847dbd3d5e312b13cfe8a90844c8f88d3aedc78 https://github.com/galaxyproject/galaxy/commit/a847dbd3d5e312b13cfe8a90844c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Fix tool report submission Commit: a6e9504dde8b5c96f6f5fc183c56d9458b996588 https://github.com/galaxyproject/galaxy/commit/a6e9504dde8b5c96f6f5fc183c56… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5303 from mvdbeek/sentry_hotfix [17.09] Fix tool report submission with sentry Compare: https://github.com/galaxyproject/galaxy/compare/a81f3e4e8c5f...a6e9504dde8b

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[galaxyproject/galaxy] a70ecd: Fix common_startup.sh bashisms
by GitHub 12 Jan '18

12 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a70ecd0147bb178b90b820d4c5cac0caa86152ab https://github.com/galaxyproject/galaxy/commit/a70ecd0147bb178b90b820d4c5ca… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Fix common_startup.sh bashisms Introduced in commit 45a25a1b8bd182cc6dff2926974681ef1bf4fc6f . This was causing this error on the `dev` branch on Ubuntu (which uses `dash`): ``` $ ./run.sh ./scripts/common_startup.sh: 69: [: dev: unexpected operator Activating virtualenv at .venv ... ``` instead of exiting with the "The Galaxy client build is out of date." message. Commit: 199457f23bf66fab7a1ca6cf86bbb215274d983c https://github.com/galaxyproject/galaxy/commit/199457f23bf66fab7a1ca6cf86bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5304 from nsoranzo/fix_common_startup.sh Fix common_startup.sh bashisms Compare: https://github.com/galaxyproject/galaxy/compare/a2f8ff21fdc2...199457f23bf6

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[galaxyproject/galaxy] cf1557: Improve the migration message when having to downg...
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cf155744662a2b6b0ce7d751f7d1429929b9a764 https://github.com/galaxyproject/galaxy/commit/cf155744662a2b6b0ce7d751f7d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/model/migrate/check.py Log Message: ----------- Improve the migration message when having to downgrade the database Commit: 58cda0ddd1663c16ba9b4772d9d2334cb4d45543 https://github.com/galaxyproject/galaxy/commit/58cda0ddd1663c16ba9b4772d9d2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/model/migrate/check.py Log Message: ----------- Slight wording tweak to migration message Commit: a2f8ff21fdc240e12c0dff2d2eb95ff7bbdc8d49 https://github.com/galaxyproject/galaxy/commit/a2f8ff21fdc240e12c0dff2d2eb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/model/migrate/check.py Log Message: ----------- Merge pull request #5299 from mvdbeek/improve_downgrade_message Improve the migration message when having to downgrade the database Compare: https://github.com/galaxyproject/galaxy/compare/79651a108011...a2f8ff21fdc2

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[galaxyproject/galaxy] bb39b7: Provide UI collection output information for subwo...
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb39b7d60b39eeae7f112edb42d9563731a725bf https://github.com/galaxyproject/galaxy/commit/bb39b7d60b39eeae7f112edb42d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Provide UI collection output information for subworkflows. This fixes #5158 and should provide more correct extension based connection information as well. Includes a backport of #4346 which fixes #3120. Commit: d1510c739492cf1e7b9d0e2d793dfb4d18d91537 https://github.com/galaxyproject/galaxy/commit/d1510c739492cf1e7b9d0e2d793d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-01 (Mon, 01 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5172 from jmchilton/1705_subworkflow_collection_outputs [17.05] Provide UI collection output information for subworkflows. Commit: a19596e3eacf63e749352f583be8774d43795d79 https://github.com/galaxyproject/galaxy/commit/a19596e3eacf63e749352f583be8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix dataset-model's edit url Commit: 9aabaa68594421e920ed6d1ac1d287e561453d8b https://github.com/galaxyproject/galaxy/commit/9aabaa68594421e920ed6d1ac1d2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M static/maps/mvc/dataset/dataset-model.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/dataset/dataset-model.js Log Message: ----------- Build client Commit: 40f9c6bb858da82e21679281d3cc644271f53eb8 https://github.com/galaxyproject/galaxy/commit/40f9c6bb858da82e21679281d3cc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js M static/maps/mvc/dataset/dataset-model.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/dataset/dataset-model.js Log Message: ----------- Merge pull request #5289 from dannon/dataset_edit_fix [17.09] Fix dataset edit link Commit: 27c9fff8b9333d67c039cdbd5c7f1840f095633d https://github.com/galaxyproject/galaxy/commit/27c9fff8b9333d67c039cdbd5c7f… Author: NCEichner <norbert.eichner(a)ur.de> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- #5187 In order to get rid of the conda error described in #5187 I raised the version number beginning from which conda is allowed to use the '--offline' parameter again to "4.4" Commit: 201c6ca8812b243d7ff824df58a3b2fd64a88289 https://github.com/galaxyproject/galaxy/commit/201c6ca8812b243d7ff824df58a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5298 from nsoranzo/release_17.09_backport_5233 [17.09] Backport #5233 Commit: a81f3e4e8c5fb06c2cd33569380a188b44a9da8a https://github.com/galaxyproject/galaxy/commit/a81f3e4e8c5fb06c2cd33569380a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Conflicts: lib/galaxy/workflow/modules.py Commit: 79651a1080112df0826cc74130f65bd793d0fdc8 https://github.com/galaxyproject/galaxy/commit/79651a1080112df0826cc74130f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/db8721e6b869...79651a108011

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[galaxyproject/galaxy] bb39b7: Provide UI collection output information for subwo...
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: bb39b7d60b39eeae7f112edb42d9563731a725bf https://github.com/galaxyproject/galaxy/commit/bb39b7d60b39eeae7f112edb42d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Provide UI collection output information for subworkflows. This fixes #5158 and should provide more correct extension based connection information as well. Includes a backport of #4346 which fixes #3120. Commit: d1510c739492cf1e7b9d0e2d793dfb4d18d91537 https://github.com/galaxyproject/galaxy/commit/d1510c739492cf1e7b9d0e2d793d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-01 (Mon, 01 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5172 from jmchilton/1705_subworkflow_collection_outputs [17.05] Provide UI collection output information for subworkflows. Commit: a81f3e4e8c5fb06c2cd33569380a188b44a9da8a https://github.com/galaxyproject/galaxy/commit/a81f3e4e8c5fb06c2cd33569380a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Conflicts: lib/galaxy/workflow/modules.py Compare: https://github.com/galaxyproject/galaxy/compare/201c6ca8812b...a81f3e4e8c5f

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[galaxyproject/galaxy] 27c9ff: #5187
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 27c9fff8b9333d67c039cdbd5c7f1840f095633d https://github.com/galaxyproject/galaxy/commit/27c9fff8b9333d67c039cdbd5c7f… Author: NCEichner <norbert.eichner(a)ur.de> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- #5187 In order to get rid of the conda error described in #5187 I raised the version number beginning from which conda is allowed to use the '--offline' parameter again to "4.4" Commit: 201c6ca8812b243d7ff824df58a3b2fd64a88289 https://github.com/galaxyproject/galaxy/commit/201c6ca8812b243d7ff824df58a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5298 from nsoranzo/release_17.09_backport_5233 [17.09] Backport #5233 Compare: https://github.com/galaxyproject/galaxy/compare/40f9c6bb858d...201c6ca8812b

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[galaxyproject/galaxy] 5c4c25: Mention how to specify the config file location
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c4c25b63d574562ea93687c95e654d5571b5710 https://github.com/galaxyproject/galaxy/commit/5c4c25b63d574562ea93687c95e6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M scripts/db_shell.py Log Message: ----------- Mention how to specify the config file location and how to do that when using ipython. Commit: db8721e6b869548039b7a4c40b7e49575d800fbb https://github.com/galaxyproject/galaxy/commit/db8721e6b869548039b7a4c40b7e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M scripts/db_shell.py Log Message: ----------- Merge pull request #5297 from mvdbeek/db_shell_doc_update Mention how to specify the config file location Compare: https://github.com/galaxyproject/galaxy/compare/c7581f867de0...db8721e6b869

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[galaxyproject/galaxy] ad925d: add infernal-cm datatype
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ad925ddfcaa205918aac2f4fb48e4b6f93edf29c https://github.com/galaxyproject/galaxy/commit/ad925ddfcaa205918aac2f4fb48e… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/infernal.py Log Message: ----------- add infernal-cm datatype Commit: 772bab983d28235e2f16c2e85803309917a1a179 https://github.com/galaxyproject/galaxy/commit/772bab983d28235e2f16c2e85803… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- simplify sniff Commit: ad3f54676943e57aa089358c2b4ec8163e824220 https://github.com/galaxyproject/galaxy/commit/ad3f54676943e57aa089358c2b4e… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- no cm count Commit: 3b394e10c9ffa13e0de1c6163c1012053d005c27 https://github.com/galaxyproject/galaxy/commit/3b394e10c9ffa13e0de1c6163c10… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- lint py3 Commit: 2c083e24e8716c8c61fab2a213d25ae928b07210 https://github.com/galaxyproject/galaxy/commit/2c083e24e8716c8c61fab2a213d2… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- lint py3 fix Commit: 0f8fbed83b4dae66529802fe98fa83737375751d https://github.com/galaxyproject/galaxy/commit/0f8fbed83b4dae66529802fe98fa… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- reorder import Commit: 22072a6cdb89b4a87b9e81274485c5ef7f2e94ee https://github.com/galaxyproject/galaxy/commit/22072a6cdb89b4a87b9e81274485… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- minor reorders Commit: f52c5de5fb838e2dac6d447605db020752332639 https://github.com/galaxyproject/galaxy/commit/f52c5de5fb838e2dac6d447605db… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/infernal.py M lib/galaxy/datatypes/msa.py Log Message: ----------- merge infernal into msa Commit: f33ee573e9b15f1479e5ab36facdcc7032a3264b https://github.com/galaxyproject/galaxy/commit/f33ee573e9b15f1479e5ab36facd… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- minor fix Commit: 5cb1cb5ec20107a95755e1b6bcb69909878d002d https://github.com/galaxyproject/galaxy/commit/5cb1cb5ec20107a95755e1b6bcb6… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- Rename class, add CM version Commit: 20278b8b31ec15bd21f3ae8ff620472644a11b41 https://github.com/galaxyproject/galaxy/commit/20278b8b31ec15bd21f3ae8ff620… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/test/infernal_model.cm Log Message: ----------- add unit-test, fix class name Commit: 86955b4b3c907412916519a75ae30eca86ed8abf https://github.com/galaxyproject/galaxy/commit/86955b4b3c907412916519a75ae3… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- remove split for cm Commit: a73d566f1fa812e4e8ce4c32baa61647e689b5ac https://github.com/galaxyproject/galaxy/commit/a73d566f1fa812e4e8ce4c32baa6… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- Dynamically set cm_version Commit: 5c415e6855987ac87bdc4318cd5e5ed512811496 https://github.com/galaxyproject/galaxy/commit/5c415e6855987ac87bdc4318cd5e… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M 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test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py A test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/data_source.py M tools/data_source/microbial_import.xml M tools/data_source/upload.py M tools/data_source/upload.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/genomespace/genomespace_importer.py M tools/phenotype_association/senatag.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into cm-datatype Commit: 9c5c7e9caa404cac1b7c1a000df5c1310775e85e https://github.com/galaxyproject/galaxy/commit/9c5c7e9caa404cac1b7c1a000df5… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- Fix Commit: 6bc2250daba23c56302e255d64ee7a8e64a4845b https://github.com/galaxyproject/galaxy/commit/6bc2250daba23c56302e255d64ee… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- to pass pylint Commit: 8e4fbe7cf35695122b77cd159b258a8e3352fa1b https://github.com/galaxyproject/galaxy/commit/8e4fbe7cf35695122b77cd159b25… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/test/infernal_model.cm Log Message: ----------- smaller cm test file Commit: a0750864a6062012a301bf612a4409659406bc54 https://github.com/galaxyproject/galaxy/commit/a0750864a6062012a301bf612a44… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- minor changes Commit: e73be6fe12f0715b275c3a75d5ce2ab66a98cb37 https://github.com/galaxyproject/galaxy/commit/e73be6fe12f0715b275c3a75d5ce… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- fix typo Commit: c7581f867de0b1386ded887f69ef10373cfb7e1b https://github.com/galaxyproject/galaxy/commit/c7581f867de0b1386ded887f69ef… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/test/infernal_model.cm Log Message: ----------- Merge pull request #4977 from mmiladi/cm-datatype add infernal-cm datatype Compare: https://github.com/galaxyproject/galaxy/compare/812f5f563047...c7581f867de0

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[galaxyproject/galaxy] 823d07: Prettier upgrade to 1.10
by GitHub 10 Jan '18

10 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 823d07d41a8e0bc495a3cf31977cb7b9ae5b77a9 https://github.com/galaxyproject/galaxy/commit/823d07d41a8e0bc495a3cf31977c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Prettier upgrade to 1.10 Commit: e88706c282a297ef251a4cfeb8adff1d17c166f8 https://github.com/galaxyproject/galaxy/commit/e88706c282a297ef251a4cfeb8ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/package.json Log Message: ----------- Prettier now supports Vue SFCs Commit: 9cddf804fa2362e7fc13acc141a55b20c7fc98ea https://github.com/galaxyproject/galaxy/commit/9cddf804fa2362e7fc13acc141a5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue Log Message: ----------- Run client-format Commit: d79d2fa4647605d2cdc36bc8e28fb2c6a4104eca https://github.com/galaxyproject/galaxy/commit/d79d2fa4647605d2cdc36bc8e28f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js Log Message: ----------- Client build. Commit: 812f5f563047e212f10bb2718552c5be16dc6f5a https://github.com/galaxyproject/galaxy/commit/812f5f563047e212f10bb2718552… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/package.json M client/yarn.lock M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js Log Message: ----------- Merge pull request #5293 from dannon/prettier_1.10 Prettier 1.10 upgrade, supports Vue components now. Compare: https://github.com/galaxyproject/galaxy/compare/aa81ccf8ac13...812f5f563047

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[galaxyproject/galaxy] a19596: Fix dataset-model's edit url
by GitHub 10 Jan '18

10 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: a19596e3eacf63e749352f583be8774d43795d79 https://github.com/galaxyproject/galaxy/commit/a19596e3eacf63e749352f583be8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix dataset-model's edit url Commit: 9aabaa68594421e920ed6d1ac1d287e561453d8b https://github.com/galaxyproject/galaxy/commit/9aabaa68594421e920ed6d1ac1d2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M static/maps/mvc/dataset/dataset-model.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/dataset/dataset-model.js Log Message: ----------- Build client Commit: 40f9c6bb858da82e21679281d3cc644271f53eb8 https://github.com/galaxyproject/galaxy/commit/40f9c6bb858da82e21679281d3cc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js M static/maps/mvc/dataset/dataset-model.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/dataset/dataset-model.js Log Message: ----------- Merge pull request #5289 from dannon/dataset_edit_fix [17.09] Fix dataset edit link Compare: https://github.com/galaxyproject/galaxy/compare/087537a7ade9...40f9c6bb858d

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[galaxyproject/galaxy] 15bc61: #5291 fix link to HTTP getgalaxy.org
by GitHub 10 Jan '18

10 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 15bc610cf06ee3aecd61cbb84e2de8a207809f9d https://github.com/galaxyproject/galaxy/commit/15bc610cf06ee3aecd61cbb84e2d… Author: selten <selten(a)users.noreply.github.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/production.md Log Message: ----------- #5291 fix link to HTTP getgalaxy.org Commit: f1f6a19a0fc87107e7429f366906a914cb543c82 https://github.com/galaxyproject/galaxy/commit/f1f6a19a0fc87107e7429f366906… Author: selten <selten(a)users.noreply.github.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/production.md Log Message: ----------- #5291 Changed text, removed Admin/GetGalaxy Commit: aa81ccf8ac1376715222243fde5566a554227d71 https://github.com/galaxyproject/galaxy/commit/aa81ccf8ac1376715222243fde55… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M doc/source/admin/production.md Log Message: ----------- Merge pull request #5295 from selten/dev #5291 fix link to HTTP getgalaxy.org Compare: https://github.com/galaxyproject/galaxy/compare/242bf89891e1...aa81ccf8ac13

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[galaxyproject/galaxy] 3b9507: Update locale.js
by GitHub 10 Jan '18

10 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b950763a715d30aa28bb26cc259ed7026fc1b2c https://github.com/galaxyproject/galaxy/commit/3b950763a715d30aa28bb26cc259… Author: steven <ishenweiyan(a)qq.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Update locale.js update zh localization Commit: cd9324ab51e33b7c0ddeaf5ebeb9ca5206706801 https://github.com/galaxyproject/galaxy/commit/cd9324ab51e33b7c0ddeaf5ebeb9… Author: steven <ishenweiyan(a)qq.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Update locale.js Commit: 3a83c1392e3546d06a45b1237422548199422576 https://github.com/galaxyproject/galaxy/commit/3a83c1392e3546d06a45b1237422… Author: steven <ishenweiyan(a)qq.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Update locale.js Commit: 2b22e4ce2517b8576f34de960a7408d1dbf1a887 https://github.com/galaxyproject/galaxy/commit/2b22e4ce2517b8576f34de960a74… Author: steven <ishenweiyan(a)qq.com> Date: 2017-12-19 (Tue, 19 Dec 2017) Log Message: ----------- Add chinese support Add simplified Chinese support Commit: 6e84fef4e0041544e63f426e654b3974160cfec6 https://github.com/galaxyproject/galaxy/commit/6e84fef4e0041544e63f426e654b… Author: steven <ishenweiyan(a)qq.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Update locale.js Add tool-panel and history-panel title translation. Commit: 9c743f2b084bb53adaed832c36b1d105ba7a9334 https://github.com/galaxyproject/galaxy/commit/9c743f2b084bb53adaed832c36b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Merge remote-tracking branch 'istevenshen/dev' into dev Commit: e2a662eb95bc54e546fd699d91f3ae1ce0beef5b https://github.com/galaxyproject/galaxy/commit/e2a662eb95bc54e546fd699d91f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Client format Commit: 242bf89891e1f95288447cbe4079ba58fd2098b1 https://github.com/galaxyproject/galaxy/commit/242bf89891e1f95288447cbe4079… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/nls/zh/locale.js Log Message: ----------- Client build. Compare: https://github.com/galaxyproject/galaxy/compare/11f434af3987...242bf89891e1

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[galaxyproject/galaxy] 489f0a: Cleanup in dataset-error.js, extra escaping.
by GitHub 09 Jan '18

09 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 489f0a84df062b5fdad3835d3666232771e5b39b https://github.com/galaxyproject/galaxy/commit/489f0a84df062b5fdad3835d3666… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-08 (Mon, 08 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Cleanup in dataset-error.js, extra escaping. Commit: 38e725ff66bfd3e5c0bceef2a937644f8b1bc8c5 https://github.com/galaxyproject/galaxy/commit/38e725ff66bfd3e5c0bceef2a937… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-08 (Mon, 08 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Template formatting. Commit: 5f3e11c02c24ca96beb3342f58bcd78ea15044f7 https://github.com/galaxyproject/galaxy/commit/5f3e11c02c24ca96beb3342f58bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-08 (Mon, 08 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- A few minor tweaks to page rendering on dataset error interface Commit: 24cfb6b52216ac9bfccf8eea02a7ff0344129e2f https://github.com/galaxyproject/galaxy/commit/24cfb6b52216ac9bfccf8eea02a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-08 (Mon, 08 Jan 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Client build. Commit: 11f434af3987ef1982dcd64c2f1a63219038c976 https://github.com/galaxyproject/galaxy/commit/11f434af3987ef1982dcd64c2f1a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Merge pull request #5279 from dannon/dataset-error-cleanup Dataset Error Interface Cleanup Compare: https://github.com/galaxyproject/galaxy/compare/14cb52ea9b0f...11f434af3987

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[galaxyproject/galaxy] da3e48: Mark rerun_with_use_cached_job as flakey
by GitHub 09 Jan '18

09 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: da3e48faa58485a5ff097d21f79470acd3c1cf34 https://github.com/galaxyproject/galaxy/commit/da3e48faa58485a5ff097d21f794… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Mark rerun_with_use_cached_job as flakey Sometimes it does not pick up the equivalent job that should exist. Will need to dig into this, but in the meantime we can allow the test to fail. Commit: 14cb52ea9b0f657aacfd712dcaeada9af15e0703 https://github.com/galaxyproject/galaxy/commit/14cb52ea9b0f657aacfd712dcaea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #5286 from mvdbeek/disable_cached_job_rerun_test Mark rerun_with_use_cached_job as flakey Compare: https://github.com/galaxyproject/galaxy/compare/00d7ec0b4237...14cb52ea9b0f

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