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

[galaxyproject/galaxy] fe87cd: Allow mapping requirements with version None to a ...
by GitHub 31 Jan '17

31 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: fe87cd889f2bdab122fccd0db99aa31af864d1db https://github.com/galaxyproject/galaxy/commit/fe87cd889f2bdab122fccd0db99a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Allow mapping requirements with version None to a specific version (so that all-in-one dependency resolution is applied) but do not match a specific requirement (i.e samtools 0.1.19) when mapping ``` - from: name: samtools version: None to: name: samtools version: 1.3.1 ``` This will only map samtools requirements that do not specify a version. If you want to override a specifically requested version, you need to include that version, i.e ``` - from: name: samtools version: None to: name: samtools version: 1.3.1 - from: name: samtools version: 0.1.19 to: name: samtools version: 1.2 ``` Commit: d3093013f95a4a0d324213f6ab4461f6d196d1fd https://github.com/galaxyproject/galaxy/commit/d3093013f95a4a0d324213f6ab44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Extend default mapping Commit: 44a90033dbe1c635e37952711e28de1016ee1090 https://github.com/galaxyproject/galaxy/commit/44a90033dbe1c635e37952711e28… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Use Null instead of None to get the non-string None value. str(from_raw.get(version)) will turn it into 'None' anyway. Commit: b92e9b509354a570424da4b1ff86a5f75bba585a https://github.com/galaxyproject/galaxy/commit/b92e9b509354a570424da4b1ff86… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Add unit tests that asserts new dependency mapping rules Commit: a30d6dfa2090096975ca614a85cde53ae9c948bb https://github.com/galaxyproject/galaxy/commit/a30d6dfa2090096975ca614a85cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Drop openbabel mapping from 2.32 to 2.4.1 (thx @bgruening) Commit: 14529b9dd56b45afe6d06babf88eb6a164c517e5 https://github.com/galaxyproject/galaxy/commit/14529b9dd56b45afe6d06babf88e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Collapse list of tool requirements after mapping With this change, the merged environment name for requirements that have been specified using multiple names (e.g. sickle (for TS) and sickle-trim (conda/docker)) will be sickle-trim if mapping sickle to sickle-trim (instead of mulled-v1-<hash>). Commit: 6ba0291eea85723514a7a983f009e4033f660ea0 https://github.com/galaxyproject/galaxy/commit/6ba0291eea85723514a7a983f009… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M config/local_conda_mapping.yml.sample M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M test/unit/tools/test_tool_deps.py Log Message: ----------- Modify representation of mapping to None. (#4) I feel that mapping from ``` - from: blast+ to: blast ``` should be the same as ``` - from: name: blast+ version: Null to: blast ``` since it should just be syntatic sugar. And I think that second version reads like it should by default apply to all versions. I feel therefore it is probably better to explicitly require stating that a mapping only applies to unversioned requirements. This commit does that by introducing the syntax: ``` - from: name: blast+ unversioned: true to: name: blast version: 1.3.4 ``` It feels better to have strongly typed entities like this than to introduce magic constants such as: ``` - from: name: blast+ version: __unversioned__ to: name: blast version: 1.3.4 ``` which is another route this could have gone I guess. Commit: ea7e1cc945cb529293a93b14612bb03f5096902a https://github.com/galaxyproject/galaxy/commit/ea7e1cc945cb529293a93b14612b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Use ToolRequirements (uses OrderedSet internally) to collapse redundant requirements instead of set to maintain the order of specified requirements. Commit: 39c03fc6a0be3b56b1972411c281b06391ac65c1 https://github.com/galaxyproject/galaxy/commit/39c03fc6a0be3b56b1972411c281… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #3509 from mvdbeek/allow_mapping_from_none [17.01] Add `unversioned` keyword to limit mappings to requirements without version Compare: https://github.com/galaxyproject/galaxy/compare/82ec7828af24...39c03fc6a0be

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[galaxyproject/galaxy] 2209b8: Fix bug in sample description from #3364.
by GitHub 31 Jan '17

31 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 2209b899b7075a5cf0f076d31248cc3ec244688e https://github.com/galaxyproject/galaxy/commit/2209b899b7075a5cf0f076d31248… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix bug in sample description from #3364. Commit: 82ec7828af24f51815dd502fab25c02dbe79e95b https://github.com/galaxyproject/galaxy/commit/82ec7828af24f51815dd502fab25… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3521 from jmchilton/fix_sample_desc_3364 [17.01] Fix sample description bug from #3364. Compare: https://github.com/galaxyproject/galaxy/compare/a8e59b7b238d...82ec7828af24

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[galaxyproject/galaxy] 1a463f: Pull build_sites out of datatypes conf.
by GitHub 31 Jan '17

31 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a463f1688673196fd7d5fd02318484bfd0bb7a9 https://github.com/galaxyproject/galaxy/commit/1a463f1688673196fd7d5fd02318… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: A config/build_sites.yml.sample M config/datatypes_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M scripts/common_startup.sh Log Message: ----------- Pull build_sites out of datatypes conf. So deployers may modify these paths and stil use the default datatypes config. This should speed up set_metadata also since each of these config files won't be loaded as part of that. Commit: bb318d36e6a2d760f93abee4a1801724244ec741 https://github.com/galaxyproject/galaxy/commit/bb318d36e6a2d760f93abee4a180… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: A config/build_sites.yml.sample M config/datatypes_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M scripts/common_startup.sh Log Message: ----------- Merge pull request #3503 from jmchilton/datatypes_build_sites Improvements to build sites configuration Compare: https://github.com/galaxyproject/galaxy/compare/80d3f735e2d0...bb318d36e6a2

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[galaxyproject/galaxy] 5ad185: Disable conda_auto_init by default for most tests.
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 5ad185590148390ec27750567273f59546eec219 https://github.com/galaxyproject/galaxy/commit/5ad185590148390ec27750567273… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Disable conda_auto_init by default for most tests. Executing framework, API, and/or selenium tests was causing Conda to be installed. This isn't needed - the only tests that test Conda dependencies are unit tests and integration tests that explicitly configure this Conda installation. Commit: a8e59b7b238d123d2407021bd7d62465fbb7d43d https://github.com/galaxyproject/galaxy/commit/a8e59b7b238d123d2407021bd7d6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Merge pull request #3517 from jmchilton/disable_testing_conda [17.01] Disable conda_auto_init by default for most tests. Compare: https://github.com/galaxyproject/galaxy/compare/8b08384be3bc...a8e59b7b238d

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[galaxyproject/galaxy] 70808b: Update committers list to reflect latest
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 70808b4b8605223f321f935343764301ead5cf1a https://github.com/galaxyproject/galaxy/commit/70808b4b8605223f321f93534376… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Update committers list to reflect latest Commit: 80d3f735e2d08eb656fc2d6dea833af088a7128b https://github.com/galaxyproject/galaxy/commit/80d3f735e2d08eb656fc2d6dea83… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #3420 from nturaga/edit_commit_list [PROCEDURES] Update committers list to reflect latest Compare: https://github.com/galaxyproject/galaxy/compare/4eb770dee584...80d3f735e2d0

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[galaxyproject/galaxy] dd77cd: Add API test for converters after toolbox reload
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 https://github.com/galaxyproject/galaxy/commit/dd77cdb62576a62ea7e8ce8e31d2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Add API test for converters after toolbox reload Commit: 78b4f8f7627a63be7ba593109c1ffd36891168ba https://github.com/galaxyproject/galaxy/commit/78b4f8f7627a63be7ba593109c1f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py Log Message: ----------- Reload converter tools after toolbox reload Commit: 36ecf28adaa3328cac3248dc7e8c3ef79211c204 https://github.com/galaxyproject/galaxy/commit/36ecf28adaa3328cac3248dc7e8c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M test/api/test_datatypes.py Log Message: ----------- Use CONVERTER_fasta_to_tabular as example converter (thx @jmchilton) Commit: e4999510ee2bc44802b4891a1a09b00489b01a9c https://github.com/galaxyproject/galaxy/commit/e4999510ee2bc44802b4891a1a09… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Merge pull request #3486 from mvdbeek/converter_reload [16.10] BUG: Reload converter tools after toolbox reload Compare: https://github.com/galaxyproject/galaxy/compare/1c0c378debde...e4999510ee2b

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[galaxyproject/galaxy] 6dd134: Give ToolRequirements a string representation for ...
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6dd1341ae09c73a11ed19b256d1f95da191f004b https://github.com/galaxyproject/galaxy/commit/6dd1341ae09c73a11ed19b256d1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Give ToolRequirements a string representation for easier debugging. Commit: ba3b00d1f813298e345c6f47bf6d6db31041c2ed https://github.com/galaxyproject/galaxy/commit/ba3b00d1f813298e345c6f47bf6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Fix integration test for default Conda mapping. It worked locally simply because I had R already installed on my system globally. Commit: 4eb770dee58433fa8a1a4008b4204c1ccb464fc6 https://github.com/galaxyproject/galaxy/commit/4eb770dee58433fa8a1a4008b420… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3508 from jmchilton/conda_mapping_test_fix Fix integration test for default Conda mapping. Compare: https://github.com/galaxyproject/galaxy/compare/68ab629723fe...4eb770dee584

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[galaxyproject/galaxy] cbba01: Disable sniffing of fastq files by default.
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: cbba01c8dc9f5303712a5c46fcee475be5e03bd8 https://github.com/galaxyproject/galaxy/commit/cbba01c8dc9f5303712a5c46fcee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Disable sniffing of fastq files by default. Start Galaxy with GALAXY_ENABLE_BETA_COMPRESSED_FASTQ_SNIFFING=1 to re-enable this. Commit: a43d7ab8f43b891b30ded632da728e9076ae03f6 https://github.com/galaxyproject/galaxy/commit/a43d7ab8f43b891b30ded632da72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Add missing compressed attribute thanks to @nsoranzo. Commit: 8b08384be3bc84f5474617e4c4dc9466ff036a67 https://github.com/galaxyproject/galaxy/commit/8b08384be3bc84f5474617e4c4dc… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3510 from jmchilton/1701_disable_compressed_fastq_sniffing [17.01] Disable compressed fastq sniffing by default. Compare: https://github.com/galaxyproject/galaxy/compare/aba3d8844b7a...8b08384be3bc

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[galaxyproject/usegalaxy-playbook] 1fb776: more 16gb tools
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/add-16gb-tools 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

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[galaxyproject/galaxy] 1c9797: explicit sniffing of FastqGz/FastqBz2 types
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 1c979769dc73e4e8824213161caa82837f340802 https://github.com/galaxyproject/galaxy/commit/1c979769dc73e4e8824213161caa… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- explicit sniffing of FastqGz/FastqBz2 types Commit: b3c9f82b1a6fa743e927e545704e868a0f100e25 https://github.com/galaxyproject/galaxy/commit/b3c9f82b1a6fa743e927e545704e… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqdsrc_to_fastq.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- Added fastq.dsrc datatype Commit: dccf20ab7968e2d67afa32470b74776fbfef3a84 https://github.com/galaxyproject/galaxy/commit/dccf20ab7968e2d67afa32470b74… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/converters/fastqdsrc_to_fastq.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- Revert "Added fastq.dsrc datatype" This reverts commit b3c9f82b1a6fa743e927e545704e868a0f100e25. Inadvertent commit to PR branch Commit: 1f818ad1d6b22f42f4c3b5599812852730e01de8 https://github.com/galaxyproject/galaxy/commit/1f818ad1d6b22f42f4c3b5599812… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- added newline to make lint happy Commit: aba3d8844b7a56e47ebbed42ec3de46debb82d75 https://github.com/galaxyproject/galaxy/commit/aba3d8844b7a56e47ebbed42ec3d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3514 from jvolkening/release_17.01 [17.01] explicit sniffing of FastqGz/FastqBz2 types Compare: https://github.com/galaxyproject/galaxy/compare/02dd2e4708e7...aba3d8844b7a

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