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
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