Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 496fa5144dc373952c0d815b844b17fef394f632 https://github.com/galaxyproject/galaxy/commit/496fa5144dc373952c0d815b844b1... Author: guerler aysam.guerler@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/ccacbb7c3b7dc453b687fb7ec332f... Author: guerler aysam.guerler@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/78a37b2a191403a87ea05fc88f890... Author: guerler aysam.guerler@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/fe87cd889f2bdab122fccd0db99aa... Author: mvdbeek m.vandenbeek@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/d3093013f95a4a0d324213f6ab446... Author: mvdbeek m.vandenbeek@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/44a90033dbe1c635e37952711e28d... Author: mvdbeek m.vandenbeek@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/f51355a183852565a857f825776bd... Author: Martin Cech cech.marten@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/b92e9b509354a570424da4b1ff86a... Author: mvdbeek m.vandenbeek@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/a30d6dfa2090096975ca614a85cde... Author: mvdbeek m.vandenbeek@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/14529b9dd56b45afe6d06babf88eb... Author: mvdbeek m.vandenbeek@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/54036e9f7d41606f40d87859c45db... Author: guerler aysam.guerler@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/1c979769dc73e4e8824213161caa8... Author: jvolkening jdv@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/b3c9f82b1a6fa743e927e545704e8... Author: jvolkening jdv@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/dccf20ab7968e2d67afa32470b747... Author: jvolkening jdv@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/1f818ad1d6b22f42f4c3b55998128... Author: jvolkening jdv@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/02dd2e4708e7167248c48b2452621... Author: John Chilton jmchilton@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/6ba0291eea85723514a7a983f009e... Author: John Chilton jmchilton@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/ea7e1cc945cb529293a93b14612bb... Author: mvdbeek m.vandenbeek@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/aba3d8844b7a56e47ebbed42ec3de... Author: Martin Cech cech.marten@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/cbba01c8dc9f5303712a5c46fcee4... Author: John Chilton jmchilton@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/a43d7ab8f43b891b30ded632da728... Author: John Chilton jmchilton@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/8b08384be3bc84f5474617e4c4dc9... Author: Marius van den Beek m.vandenbeek@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/5ad185590148390ec27750567273f... Author: John Chilton jmchilton@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/a8e59b7b238d123d2407021bd7d62... Author: Martin Cech cech.marten@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/2209b899b7075a5cf0f076d31248c... Author: John Chilton jmchilton@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/82ec7828af24f51815dd502fab25c... Author: Martin Cech cech.marten@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/39c03fc6a0be3b56b1972411c281b... Author: Dannon Baker dannon.baker@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/21aa0d850f774e94b10a5e5baaceb... Author: Martin Cech cech.marten@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