galaxy-commits January 2018

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[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 16 Jan '18

16 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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galaxy-commits January 2018