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

[galaxyproject/galaxy] ada16d: Only read 6 bytes.
by GitHub 01 Feb '17

01 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ada16d87484c7be9d82d2f94c1643df9e66b5eca https://github.com/galaxyproject/galaxy/commit/ada16d87484c7be9d82d2f94c164… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Only read 6 bytes. Fixes #3529 Commit: c5da4f0f001d5d236ca7c07c0a5fe55bdab21135 https://github.com/galaxyproject/galaxy/commit/c5da4f0f001d5d236ca7c07c0a5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3531 from erasche/fix-3529 Fix unbounded readline in genbank datatype Compare: https://github.com/galaxyproject/galaxy/compare/21aa0d850f77...c5da4f0f001d

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[galaxyproject/galaxy] 58241e: Rebuild client for 17.01 with latest node.
by GitHub 01 Feb '17

01 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 58241e8dcb71500d399dbe2089f5b20f1eb89b53 https://github.com/galaxyproject/galaxy/commit/58241e8dcb71500d399dbe2089f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Rebuild client for 17.01 with latest node. Commit: 9dc1bbd3bc4697f5fbf1e183883aba9277058706 https://github.com/galaxyproject/galaxy/commit/9dc1bbd3bc4697f5fbf1e183883a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Merge pull request #3535 from dannon/minor_fix [17.01] Rebuild client for 17.01 with latest node. Compare: https://github.com/galaxyproject/galaxy/compare/39c03fc6a0be...9dc1bbd3bc46

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[galaxyproject/galaxy] 496fa5: Improve dataset state information in selection fie...
by GitHub 01 Feb '17

01 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 496fa5144dc373952c0d815b844b17fef394f632 https://github.com/galaxyproject/galaxy/commit/496fa5144dc373952c0d815b844b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Improve dataset state information in selection fields Commit: ccacbb7c3b7dc453b687fb7ec332f4d6793d689d https://github.com/galaxyproject/galaxy/commit/ccacbb7c3b7dc453b687fb7ec332… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use dataset matcher for unhidden datasets only Commit: 78a37b2a191403a87ea05fc88f890504fad400c4 https://github.com/galaxyproject/galaxy/commit/78a37b2a191403a87ea05fc88f89… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Fix test case 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: f51355a183852565a857f825776bd38321cf2ff8 https://github.com/galaxyproject/galaxy/commit/f51355a183852565a857f825776b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3506 from martenson/release_17.01 [17.01] Add sam_to_bam to list of tools requiring Galaxy's environment. 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: 54036e9f7d41606f40d87859c45dbc35f794b2b3 https://github.com/galaxyproject/galaxy/commit/54036e9f7d41606f40d87859c45d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M test/unit/tools/test_data_parameters.py Log Message: ----------- Fix test case for deleted mock hdas 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: 02dd2e4708e7167248c48b2452621cf31a6bdba6 https://github.com/galaxyproject/galaxy/commit/02dd2e4708e7167248c48b245262… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge pull request #3495 from guerler/fix_dataset_label [17.01] Properly label hidden datasets in dataset selectors 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: 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 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. 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. 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. 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 Commit: 21aa0d850f774e94b10a5e5baacebead35963f0b https://github.com/galaxyproject/galaxy/commit/21aa0d850f774e94b10a5e5baace… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/datatypes/sequence.py 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 lib/galaxy/tools/parameters/basic.py M test/base/driver_util.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #3528 from galaxyproject/release_17.01 Merge Release 17.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/bb318d36e6a2...21aa0d850f77

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