February 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f53b64: WIP: Fix for conda=4.3
by GitHub 20 Feb '17

20 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: f53b6474828d1f8ab1170630ce5851bb913ebec7 https://github.com/galaxyproject/galaxy/commit/f53b6474828d1f8ab1170630ce58… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- WIP: Fix for conda=4.3 Commit: d37ed7e7dadcf568b22836f477ce5afd2a377af7 https://github.com/galaxyproject/galaxy/commit/d37ed7e7dadcf568b22836f477ce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Adjust offline fix to work for a broader range of potential target Condas. This logic could in theory be backported all the way to 16.01 I suppose now. Commit: 1e3c9ab945c4616510b5b4ff2726aab89585bef4 https://github.com/galaxyproject/galaxy/commit/1e3c9ab945c4616510b5b4ff2726… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- More revisions to fixing --offline mode to Conda. Incorporate package extraction fixes thanks to @nsoranzo, the fix for version 4.1 and 4.0 thanks to @mvdbeek, a comment for @bgruening and a new test tool that makes it a bit easier to test this. Commit: 0024aa458216589589d35b9366c6347c0c280860 https://github.com/galaxyproject/galaxy/commit/0024aa458216589589d35b9366c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M test/functional/tools/mulled_example_multi_incomplete.xml Log Message: ----------- Add a clarification to new test tool. Commit: f6cc1dcf077f9d98c38afdd93d47e60c42ac06e5 https://github.com/galaxyproject/galaxy/commit/f6cc1dcf077f9d98c38afdd93d47… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3632 from jmchilton/conda_43_fix [17.01] Fix Conda --offline logic for bug in 4.0,4.1,4.3. Compare: https://github.com/galaxyproject/galaxy/compare/851f08cb00ea...f6cc1dcf077f

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[galaxyproject/galaxy] 409f50: Add default docker_connect_port to interactive env...
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 409f50e282885a686b2cdbe75bfe5a5f0e8dde38 https://github.com/galaxyproject/galaxy/commit/409f50e282885a686b2cdbe75bfe… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Add default docker_connect_port to interactive environments config dictionary. Commit: 851f08cb00eac7582a90bafe660b561ebea4c50b https://github.com/galaxyproject/galaxy/commit/851f08cb00eac7582a90bafe660b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3631 from blankenberg/gie-jupyter-fix-17.01 [17.01] Add default docker_connect_port to interactive environments config dictionary. Commit: 430ac221baea4c18af247eee8e9106869a570390 https://github.com/galaxyproject/galaxy/commit/430ac221baea4c18af247eee8e91… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/28089a3ae1ea...430ac221baea

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[galaxyproject/galaxy] 409f50: Add default docker_connect_port to interactive env...
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 409f50e282885a686b2cdbe75bfe5a5f0e8dde38 https://github.com/galaxyproject/galaxy/commit/409f50e282885a686b2cdbe75bfe… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Add default docker_connect_port to interactive environments config dictionary. Commit: 851f08cb00eac7582a90bafe660b561ebea4c50b https://github.com/galaxyproject/galaxy/commit/851f08cb00eac7582a90bafe660b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3631 from blankenberg/gie-jupyter-fix-17.01 [17.01] Add default docker_connect_port to interactive environments config dictionary. Compare: https://github.com/galaxyproject/galaxy/compare/56f7af455c56...851f08cb00ea

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[galaxyproject/usegalaxy-playbook] 1fb776: more 16gb tools
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1fb7764538cc15c7ddc6b474753c333b447295ab https://github.com/galaxyproject/usegalaxy-playbook/commit/1fb7764538cc15c7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- more 16gb tools add sailfish, weightedaverage and cummerbund Commit: 2e3403866b618fa15a9cc34b8c6e1bb8d30c6113 https://github.com/galaxyproject/usegalaxy-playbook/commit/2e3403866b618fa1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Merge pull request #22 from galaxyproject/add-16gb-tools allocate more 16gb tools Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/2e21c55a4645...…

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[galaxyproject/galaxy] e5da52: Fix kombu documentation link, add a tiny bit more ...
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5da52e388af093e432efeae9f395a7f92ce97da https://github.com/galaxyproject/galaxy/commit/e5da52e388af093e432efeae9f39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix kombu documentation link, add a tiny bit more description to handle the old TODO. Commit: 28089a3ae1ea4eb8be62364aaaef65ae019dc127 https://github.com/galaxyproject/galaxy/commit/28089a3ae1ea4eb8be62364aaaef… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3629 from dannon/kombu_url_fix Fix kombu documentation link in galaxy.ini.sample Compare: https://github.com/galaxyproject/galaxy/compare/2ff6f910373a...28089a3ae1ea

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[galaxyproject/galaxy] 792bd4: Implementation of slow query logging. Disabled by...
by GitHub 17 Feb '17

17 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 792bd4f8835e9aef355a904b773f208a022e5e95 https://github.com/galaxyproject/galaxy/commit/792bd4f8835e9aef355a904b773f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Implementation of slow query logging. Disabled by default. Commit: 9135226ae40dd2222172fd6883511f682c72f7a4 https://github.com/galaxyproject/galaxy/commit/9135226ae40dd2222172fd688351… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Aarrghs spacing. Commit: 42d2a1a4e33b28c98faef4f003edebb600710562 https://github.com/galaxyproject/galaxy/commit/42d2a1a4e33b28c98faef4f003ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add forgotten sample change. Commit: 28fe37c977b18d83d91e7a1d604112f62857073f https://github.com/galaxyproject/galaxy/commit/28fe37c977b18d83d91e7a1d6041… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Style tweaks. My flake8-in-editor had silently died and was not warning me anymore, super. Commit: b14dccab631b2a68ca0131ceca27426668d9b2e2 https://github.com/galaxyproject/galaxy/commit/b14dccab631b2a68ca0131ceca27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Import formatting... Commit: 56f7af455c5638aef16d2fd7ac07cd0644f7009a https://github.com/galaxyproject/galaxy/commit/56f7af455c5638aef16d2fd7ac07… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3625 from dannon/backport_query_logging [17.01] Usable slow query logging Commit: 2ff6f910373a2eaf547472f8b4be7f92cda495bb https://github.com/galaxyproject/galaxy/commit/2ff6f910373a2eaf547472f8b4be… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f6649f890499...2ff6f910373a

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[galaxyproject/galaxy] 792bd4: Implementation of slow query logging. Disabled by...
by GitHub 16 Feb '17

16 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 792bd4f8835e9aef355a904b773f208a022e5e95 https://github.com/galaxyproject/galaxy/commit/792bd4f8835e9aef355a904b773f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Implementation of slow query logging. Disabled by default. Commit: 9135226ae40dd2222172fd6883511f682c72f7a4 https://github.com/galaxyproject/galaxy/commit/9135226ae40dd2222172fd688351… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Aarrghs spacing. Commit: 42d2a1a4e33b28c98faef4f003edebb600710562 https://github.com/galaxyproject/galaxy/commit/42d2a1a4e33b28c98faef4f003ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add forgotten sample change. Commit: 28fe37c977b18d83d91e7a1d604112f62857073f https://github.com/galaxyproject/galaxy/commit/28fe37c977b18d83d91e7a1d6041… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Style tweaks. My flake8-in-editor had silently died and was not warning me anymore, super. Commit: b14dccab631b2a68ca0131ceca27426668d9b2e2 https://github.com/galaxyproject/galaxy/commit/b14dccab631b2a68ca0131ceca27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Import formatting... Commit: 56f7af455c5638aef16d2fd7ac07cd0644f7009a https://github.com/galaxyproject/galaxy/commit/56f7af455c5638aef16d2fd7ac07… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3625 from dannon/backport_query_logging [17.01] Usable slow query logging Compare: https://github.com/galaxyproject/galaxy/compare/d2ec75084b2e...56f7af455c56

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[galaxyproject/galaxy] 0e9eb7: deprecate repair repository feature
by GitHub 16 Feb '17

16 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0e9eb78636da19c68ff3c981ff8090b63a7d11ae https://github.com/galaxyproject/galaxy/commit/0e9eb78636da19c68ff3c981ff80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- deprecate repair repository feature Commit: 29d229cedd697ff79595b223d651dd0d97ded457 https://github.com/galaxyproject/galaxy/commit/29d229cedd697ff79595b223d651… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Merge pull request #3615 from martenson/release_17.01 [17.01] deprecate repair repository feature Commit: ac191f5f2a10c003788a291501331b68fb521bc7 https://github.com/galaxyproject/galaxy/commit/ac191f5f2a10c003788a29150133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- [17.01] Make active_datasets_children_and_roles just active_datasets_and_roles. I guess somewhere in the tool building process we eliminated children from appearing the form. Remove unused code that used the children selector in the tool form. Commit: eb42d130d34c9393f3386ba115de6fe561e9ef18 https://github.com/galaxyproject/galaxy/commit/eb42d130d34c9393f3386ba115de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Fix unit tests for that last commit. Commit: d2ec75084b2eeae30ce61168462fec03f1211b6e https://github.com/galaxyproject/galaxy/commit/d2ec75084b2eeae30ce61168462f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #3624 from jmchilton/active_children_drop [17.01] Drop children from query that prefetches data for dataset matching. Commit: f6649f890499a2e4569057e4b1921f0c95426e11 https://github.com/galaxyproject/galaxy/commit/f6649f890499a2e4569057e4b192… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/89e32ee526e7...f6649f890499

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[galaxyproject/galaxy] ac191f: [17.01] Make active_datasets_children_and_roles ju...
by GitHub 16 Feb '17

16 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: ac191f5f2a10c003788a291501331b68fb521bc7 https://github.com/galaxyproject/galaxy/commit/ac191f5f2a10c003788a29150133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- [17.01] Make active_datasets_children_and_roles just active_datasets_and_roles. I guess somewhere in the tool building process we eliminated children from appearing the form. Remove unused code that used the children selector in the tool form. Commit: eb42d130d34c9393f3386ba115de6fe561e9ef18 https://github.com/galaxyproject/galaxy/commit/eb42d130d34c9393f3386ba115de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Fix unit tests for that last commit. Commit: d2ec75084b2eeae30ce61168462fec03f1211b6e https://github.com/galaxyproject/galaxy/commit/d2ec75084b2eeae30ce61168462f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #3624 from jmchilton/active_children_drop [17.01] Drop children from query that prefetches data for dataset matching. Compare: https://github.com/galaxyproject/galaxy/compare/29d229cedd69...d2ec75084b2e

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[galaxyproject/galaxy] be5eaf: Util to encode or decode values
by GitHub 15 Feb '17

15 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be5eaf4881b9624c67a7e3125dbb080032502477 https://github.com/galaxyproject/galaxy/commit/be5eaf4881b9624c67a7e3125dbb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: A scripts/cookie.py Log Message: ----------- Util to encode or decode values Commit: 6849752fb68b018aaf30f61d9d3c564894ed9e2b https://github.com/galaxyproject/galaxy/commit/6849752fb68b018aaf30f61d9d3c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: R scripts/cookie.py A scripts/secret_decoder_ring.py Log Message: ----------- Rename, Strip F for Folder Commit: fb2450ff33ebdbdeb3f1205bdc58c38519921e7a https://github.com/galaxyproject/galaxy/commit/fb2450ff33ebdbdeb3f1205bdc58… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M scripts/secret_decoder_ring.py Log Message: ----------- document scriptg Commit: 89e32ee526e7f2ebc64be8bd46337a6edef78cab https://github.com/galaxyproject/galaxy/commit/89e32ee526e7f2ebc64be8bd4633… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: A scripts/secret_decoder_ring.py Log Message: ----------- Merge pull request #3622 from erasche/encode-decode-util Util to encode or decode values Compare: https://github.com/galaxyproject/galaxy/compare/43f2a648230b...89e32ee526e7

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