- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 6af39a: Update ansible-common-roles submodule
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6af39a55ffde93c80f69fdc136c3b640d4fa2cd4 https://github.com/galaxyproject/usegalaxy-playbook/commit/6af39a55ffde93c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M common_roles Log Message: ----------- Update ansible-common-roles submodule

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[galaxyproject/usegalaxy-playbook] b65bef: Update Main
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b65bef9dc17124285c8417e0bdb1914693d0311a https://github.com/galaxyproject/usegalaxy-playbook/commit/b65bef9dc1712428… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] ddcbd8: add jenkins documentation tasks for release issue
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ddcbd8ba02b628defc3c1593e402769621798ac4 https://github.com/galaxyproject/galaxy/commit/ddcbd8ba02b628defc3c1593e402… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- add jenkins documentation tasks for release issue Commit: 3681dae83808e7a683f3d717151e10002b0b4b58 https://github.com/galaxyproject/galaxy/commit/3681dae83808e7a683f3d717151e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3523 from martenson/tweak-bootstrap-template add jenkins documentation tasks to the release issue Compare: https://github.com/galaxyproject/galaxy/compare/c5da4f0f001d...3681dae83808

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[galaxyproject/galaxy] c60233: Fix for rerunning a job when the tool does not exi...
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: c602336cc82fe60c54d10834c26fb8b0eafe81b0 https://github.com/galaxyproject/galaxy/commit/c602336cc82fe60c54d10834c26f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix for rerunning a job when the tool does not exist. Commit: f1062afa55c486a0b35418bf7e7e988136c78cb6 https://github.com/galaxyproject/galaxy/commit/f1062afa55c486a0b35418bf7e7e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #3538 from blankenberg/fix-rerun-no-tool [17.01] Fix for rerunning a job when the tool does not exist. Compare: https://github.com/galaxyproject/galaxy/compare/2322bc1ff59e...f1062afa55c4

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[galaxyproject/galaxy] 840c3b: Fix integration test for default Conda mapping.
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 840c3b0fd846ea5fb58fb34378717aeadea7e81a https://github.com/galaxyproject/galaxy/commit/840c3b0fd846ea5fb58fb3437871… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 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: 2322bc1ff59e85fb4f9db281d04b96e124dd73aa https://github.com/galaxyproject/galaxy/commit/2322bc1ff59e85fb4f9db281d04b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3541 from jmchilton/backport_3508 [17.01] Fix integration test for default Conda mapping. Compare: https://github.com/galaxyproject/galaxy/compare/da0affd45d4f...2322bc1ff59e

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[galaxyproject/galaxy] a7cc18: Fix tools that use Galaxy sequence utilities for #...
by GitHub 01 Feb '17

01 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: a7cc18d616a2fe020d1946eac91ab248f9a1c995 https://github.com/galaxyproject/galaxy/commit/a7cc18d616a2fe020d1946eac91a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix tools that use Galaxy sequence utilities for #3364. Thanks to @peterjc for reporting and @martenson for grepping. xref #minor #3364 Commit: da0affd45d4fb5479d0e0adcc4efa147bee41e63 https://github.com/galaxyproject/galaxy/commit/da0affd45d4fb5479d0e0adcc4ef… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3542 from jmchilton/more_python_preservation [17.01] Fix tools that use Galaxy sequence utilities for #3364. Compare: https://github.com/galaxyproject/galaxy/compare/bb15a431f006...da0affd45d4f

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[galaxyproject/galaxy] da7fed: Fix wiggle to wiggle2simple1 for Python path chang...
by GitHub 01 Feb '17

01 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: da7fed47445d8d1483eb456f32af19a0b0ff5412 https://github.com/galaxyproject/galaxy/commit/da7fed47445d8d1483eb456f32af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix wiggle to wiggle2simple1 for Python path changes in #3364. Fixes #3539. #minor Commit: bb15a431f006dfbe0d9777529300b8e1981fc988 https://github.com/galaxyproject/galaxy/commit/bb15a431f006dfbe0d9777529300… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3540 from jmchilton/wiggle_fix_1701 [17.01] Fix wiggle to wiggle2simple1 for Python path changes in #3364. Compare: https://github.com/galaxyproject/galaxy/compare/3858528d90c1...bb15a431f006

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[galaxyproject/galaxy] a121b8: Only read 6 bytes.
by GitHub 01 Feb '17

01 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: a121b889ef584086c96c6b9230198b3e2a04d6f6 https://github.com/galaxyproject/galaxy/commit/a121b889ef584086c96c6b923019… 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: 3858528d90c1380ae33c7e6087ee3ee1a9bb85f9 https://github.com/galaxyproject/galaxy/commit/3858528d90c1380ae33c7e6087ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3537 from jmchilton/backport_genbank_fix [17.01] Backport of fix unbounded readline in genbank datatype Compare: https://github.com/galaxyproject/galaxy/compare/9dc1bbd3bc46...3858528d90c1

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[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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[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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[galaxyproject/usegalaxy-playbook] 4e1e2d: Run kraken on multi on main
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4e1e2d7f8ed03ab5b779992216b4f1a1df50fcfa https://github.com/galaxyproject/usegalaxy-playbook/commit/4e1e2d7f8ed03ab5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Run kraken on multi on main

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[galaxyproject/usegalaxy-playbook] 11d622: Mutable config changes
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 11d6228991affe1b8d4bd2e18fea3b86c4bc49fc https://github.com/galaxyproject/usegalaxy-playbook/commit/11d6228991affe1b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable config changes Commit: 708381c3800b6115e5e4d447b5a36699721f7389 https://github.com/galaxyproject/usegalaxy-playbook/commit/708381c3800b6115… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M production/group_vars/galaxywebservers.yml Log Message: ----------- Add docker_connect_port workaround Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/62539b46cf01...…

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[galaxyproject/galaxy] f3af2a: jsonify initial value when returned through to_dic...
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3af2a06c3af09a8c96283e133910b32659916bd https://github.com/galaxyproject/galaxy/commit/f3af2a06c3af09a8c96283e13391… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- jsonify initial value when returned through to_dict caller Commit: 98cd33d4ae70606d10ce2d4602663f6d5ef632fe https://github.com/galaxyproject/galaxy/commit/98cd33d4ae70606d10ce2d460266… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use security Commit: 68ab629723fe5ab900d115d1e6bf1b619de5a2c7 https://github.com/galaxyproject/galaxy/commit/68ab629723fe5ab900d115d1e6bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3513 from guerler/jsonify_initial_value_in_dict jsonify initial value when returned through to_dict caller Compare: https://github.com/galaxyproject/galaxy/compare/04a7ce6f1016...68ab629723fe

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[galaxyproject/galaxy] 496fa5: Improve dataset state information in selection fie...
by GitHub 30 Jan '17

30 Jan '17

Branch: refs/heads/release_17.01 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: 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/f51355a18385...02dd2e4708e7

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