February 2019 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] d710bb: Discriminate data managers and allow managed testing
by Nicola Soranzo 15 Feb '19

15 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d710bb860b5802a64420eb3d5e1ebac6ac88d4ea https://github.com/galaxyproject/galaxy/commit/d710bb860b5802a64420eb3d5e1e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/loader_directory.py Log Message: ----------- Discriminate data managers and allow managed testing I am not a big fan of the heuristic in which we fall back to loading the data manager tool relative to the data_manager_conf.xml file, but I don't really see a better way here. Commit: 06d1e5a8b22072bd1de9961bcfcf051a86b90f5f https://github.com/galaxyproject/galaxy/commit/06d1e5a8b22072bd1de9961bcfcf… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- fix the name of presevered test-data Commit: 740fc8594edf6e15fdecdc3d1f30be259dc7dea2 https://github.com/galaxyproject/galaxy/commit/740fc8594edf6e15fdecdc3d1f30… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- improve test error message Commit: f311ebd1e2c237f7dc5b10f67f20aea28921877c https://github.com/galaxyproject/galaxy/commit/f311ebd1e2c237f7dc5b10f67f20… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- mention planemo explicitly Commit: f3208503f69bae63ef48e18deb85e7aa974e20c5 https://github.com/galaxyproject/galaxy/commit/f3208503f69bae63ef48e18deb85… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js Log Message: ----------- Drop 'fade in' classes on iframe; prefer static display without extra animations and fixes opacity issue from biostar. Commit: bfeb2727573a6c1c77551369bf46acf93d78190b https://github.com/galaxyproject/galaxy/commit/bfeb2727573a6c1c77551369bf46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/style/scss/base.scss Log Message: ----------- drop redundant communication server frame styles. Commit: b29b8b5c17f4126b0af597c0bccac850767f5aff https://github.com/galaxyproject/galaxy/commit/b29b8b5c17f4126b0af597c0bcca… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js Log Message: ----------- Use standard bootstrap classes for sizing here since it's only used in one spot. Commit: 62d8d808eb096daa4c99bdefd3c0aabaa3a59e56 https://github.com/galaxyproject/galaxy/commit/62d8d808eb096daa4c99bdefd3c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #7331 from mvdbeek/test_data_managers [19.01] Discriminate data managers and allow managed testing Commit: 45d06acbc8f31bdeab7b895d3fadf71d4a9aaa84 https://github.com/galaxyproject/galaxy/commit/45d06acbc8f31bdeab7b895d3fad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/style/scss/base.scss Log Message: ----------- Merge pull request #7354 from dannon/comm_server_fixes [19.01] Communication Server Display Fixes Commit: 728ff2075de24fc2386ae925efd8fde885d959db https://github.com/galaxyproject/galaxy/commit/728ff2075de24fc2386ae925efd8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Merge pull request #7352 from bgruening/test_data_fix fix the filename of saved test-data Commit: b67dc2ba24ec0c712db693cb8859e6eb703d724e https://github.com/galaxyproject/galaxy/commit/b67dc2ba24ec0c712db693cb8859… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Merge pull request #7353 from bgruening/improve_err_message Improve error message during tool testing Commit: c1a6a2a48f4c8bdf6682b8ab842a0cd391d40ca9 https://github.com/galaxyproject/galaxy/commit/c1a6a2a48f4c8bdf6682b8ab842a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-15 (Fri, 15 Feb 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/style/scss/base.scss M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/380438411dca...c1a6a2a48f4c

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[galaxyproject/galaxy] 740fc8: improve test error message
by Dannon 14 Feb '19

14 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 740fc8594edf6e15fdecdc3d1f30be259dc7dea2 https://github.com/galaxyproject/galaxy/commit/740fc8594edf6e15fdecdc3d1f30… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- improve test error message Commit: f311ebd1e2c237f7dc5b10f67f20aea28921877c https://github.com/galaxyproject/galaxy/commit/f311ebd1e2c237f7dc5b10f67f20… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- mention planemo explicitly Commit: b67dc2ba24ec0c712db693cb8859e6eb703d724e https://github.com/galaxyproject/galaxy/commit/b67dc2ba24ec0c712db693cb8859… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Merge pull request #7353 from bgruening/improve_err_message Improve error message during tool testing Compare: https://github.com/galaxyproject/galaxy/compare/728ff2075de2...b67dc2ba24ec

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[galaxyproject/galaxy] 1a5fda: Add --force_path_paste argument to tool test verif...
by Dannon 14 Feb '19

14 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a5fda5dc200ba0be428cf2d070fb0f53806b7bd https://github.com/galaxyproject/galaxy/commit/1a5fda5dc200ba0be428cf2d070f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/script.py Log Message: ----------- Add --force_path_paste argument to tool test verify script. Reverts small changes in https://github.com/galaxyproject/galaxy/pull/7160 and brings in option added in https://github.com/galaxyproject/galaxy-lib/pull/137. Though #7160 made huge strides in usability of this stuff, I still like making strides toward pasting paths since I believe this is the long term direction this code should move in (https://github.com/galaxyproject/galaxy/pull/7160#issuecomment-450751074) Some people (@bgruening) don't even think Galaxy should have a copy of the test data - so that will even more encourage pasting URIs. Commit: 380438411dca18d8e374cc720e17972b1f7c73ea https://github.com/galaxyproject/galaxy/commit/380438411dca18d8e374cc720e17… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/script.py Log Message: ----------- Merge pull request #7356 from jmchilton/force_path_paste Add --force_path_paste argument to tool test verify script. Compare: https://github.com/galaxyproject/galaxy/compare/9d80059fd6e7...380438411dca

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[galaxyproject/galaxy] 25f84b: Stronger ToolProvidedMetadata abstraction.
by John Chilton 14 Feb '19

14 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 25f84b69b6a8cf0d5cccd12aceba9b50dfe3e765 https://github.com/galaxyproject/galaxy/commit/25f84b69b6a8cf0d5cccd12aceba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-15 (Tue, 15 Jan 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py A lib/galaxy/tools/provided_metadata.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Stronger ToolProvidedMetadata abstraction. - Move to its own file (goal is to be importable from set_metadata without baggage from tools and jobs modules). - Proper interface with some basic documentation. Commit: b0eed2238558ea860c7a07953ad73a3e04c21bae https://github.com/galaxyproject/galaxy/commit/b0eed2238558ea860c7a07953ad7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M lib/galaxy/tools/provided_metadata.py Log Message: ----------- Update lib/galaxy/tools/provided_metadata.py Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: b2cebdeec159e9557a6305e4a3957afd92a5730e https://github.com/galaxyproject/galaxy/commit/b2cebdeec159e9557a6305e4a395… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M lib/galaxy/tools/provided_metadata.py Log Message: ----------- Update lib/galaxy/tools/provided_metadata.py Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: 9d80059fd6e78672593ef6d63a339612bef6031f https://github.com/galaxyproject/galaxy/commit/9d80059fd6e78672593ef6d63a33… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py A lib/galaxy/tools/provided_metadata.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #7156 from jmchilton/tool_provided_metadata Stronger ToolProvidedMetadata abstraction. Compare: https://github.com/galaxyproject/galaxy/compare/9b2f3af6f396...9d80059fd6e7

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[galaxyproject/galaxy] 6beeec: job script returns tool exit code in any case
by John Chilton 14 Feb '19

14 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6beeec836f6c6ab479700e6a1e1accbe5069dacf https://github.com/galaxyproject/galaxy/commit/6beeec836f6c6ab479700e6a1e1a… Author: M Bernt <m.bernt(a)ufz.de> Date: 2019-01-02 (Wed, 02 Jan 2019) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- job script returns tool exit code in any case Commit: 9b2f3af6f3967ab172cb5bbaa527ee622dd8fcf5 https://github.com/galaxyproject/galaxy/commit/9b2f3af6f3967ab172cb5bbaa527… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #7147 from bernt-matthias/topic/job_script_exit_code make job script actually return tool exit code Compare: https://github.com/galaxyproject/galaxy/compare/00652f0b3a94...9b2f3af6f396

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[galaxyproject/galaxy] b18aa1: group: don't remove empty cells at the begin/start...
by John Chilton 14 Feb '19

14 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b18aa199aa57e87ef62013f5c4542f7491ec9b19 https://github.com/galaxyproject/galaxy/commit/b18aa199aa57e87ef62013f5c454… Author: M Bernt <m.bernt(a)ufz.de> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M tools/stats/grouping.py Log Message: ----------- group: don't remove empty cells at the begin/start of lines currently group removes empty cells at the begin and end of lines additionally the sort command line is changed (hoping that this looks a bit more obvious) Commit: bc86e37d85ee09dad5ddbb4f4d25673c7707ea10 https://github.com/galaxyproject/galaxy/commit/bc86e37d85ee09dad5ddbb4f4d25… Author: bernt(a)informatik.uni-leipzig.de <bernt(a)informatik.uni-leipzig.de> Date: 2019-01-12 (Sat, 12 Jan 2019) Changed paths: A test-data/groupby_out1.dat A test-data/groupby_out2.dat A test-data/groupby_out3.tabular A test-data/groupby_out4.tabular M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- groupby: reenabled tests and added some, more bugfix - make script exit with code 1 in case of error - removed one more strip - adapted tool syntax to best practices Commit: 00652f0b3a9442d875266f1fd7856ec54c2eae81 https://github.com/galaxyproject/galaxy/commit/00652f0b3a9442d875266f1fd785… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: A test-data/groupby_out1.dat A test-data/groupby_out2.dat A test-data/groupby_out3.tabular A test-data/groupby_out4.tabular M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge pull request #7205 from bernt-matthias/topic/grouping-w-emptycells group: don't remove empty cells at the begin/start of lines Compare: https://github.com/galaxyproject/galaxy/compare/5bf87645e225...00652f0b3a94

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[galaxyproject/galaxy] ead622: Eliminate web framework import in history export.
by Martin Cech 14 Feb '19

14 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ead62233bf3ec1ed30584a1b7f0884e25a19292a https://github.com/galaxyproject/galaxy/commit/ead62233bf3ec1ed30584a1b7f08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Eliminate web framework import in history export. Commit: 5bf87645e225d2548c31d2b101d246d5a81b7474 https://github.com/galaxyproject/galaxy/commit/5bf87645e225d2548c31d2b101d2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #7358 from jmchilton/framework_out_export Eliminate web framework import in history export. Compare: https://github.com/galaxyproject/galaxy/compare/724125a5d384...5bf87645e225

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[galaxyproject/galaxy] 06d1e5: fix the name of presevered test-data
by John Chilton 14 Feb '19

14 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 06d1e5a8b22072bd1de9961bcfcf051a86b90f5f https://github.com/galaxyproject/galaxy/commit/06d1e5a8b22072bd1de9961bcfcf… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- fix the name of presevered test-data Commit: 728ff2075de24fc2386ae925efd8fde885d959db https://github.com/galaxyproject/galaxy/commit/728ff2075de24fc2386ae925efd8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Merge pull request #7352 from bgruening/test_data_fix fix the filename of saved test-data Compare: https://github.com/galaxyproject/galaxy/compare/45d06acbc8f3...728ff2075de2

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[galaxyproject/usegalaxy-playbook] 98302d: Install wrappers for bedtools 2.27.0
by Dave B. 14 Feb '19

14 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 98302d7abdf0cef96cd0b692131b49f0631a15d2 https://github.com/galaxyproject/usegalaxy-playbook/commit/98302d7abdf0cef9… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Install wrappers for bedtools 2.27.0

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[galaxyproject/usegalaxy-playbook] 7cf076: update TTS and MTS
by Martin Cech 14 Feb '19

14 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7cf0769e688848efdeffb0bdbdb314a39e9978b3 https://github.com/galaxyproject/usegalaxy-playbook/commit/7cf0769e688848ef… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-14 (Thu, 14 Feb 2019) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update TTS and MTS

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