Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a831033ed820e3f1220d9d326f8bd8079c390f9 https://github.com/galaxyproject/galaxy/commit/4a831033ed820e3f1220d9d326f8b... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-07-26 (Tue, 26 Jul 2016)

Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Generate metadata in separate conda environment

Galaxy supports generating metadata in a separate command (enable beta_tool_command_isolation). This command has its own dependency resolution, that may interfere with thedependency resolution of the actual tool, if the same environment is being used. With this PR we create a new environment when resolving metadata dependencies with conda, that will be active only for metadata generation.

Commit: 28da4b6371b23c69d15e7fc59473d4bde5639fde https://github.com/galaxyproject/galaxy/commit/28da4b6371b23c69d15e7fc59473d... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2016-07-26 (Tue, 26 Jul 2016)

Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py

Log Message: ----------- Fix whitespace and comma use

Commit: f8cf81d73693e5f075b6c9e612244221bbd6e5bb https://github.com/galaxyproject/galaxy/commit/f8cf81d73693e5f075b6c9e612244... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-07-26 (Tue, 26 Jul 2016)

Changed paths: M .ci/flake8_blacklist.txt

Log Message: ----------- Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore.

Commit: f0024d64e15815dcb6c2ac027ed5fb2977651e64 https://github.com/galaxyproject/galaxy/commit/f0024d64e15815dcb6c2ac027ed5f... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-07-26 (Tue, 26 Jul 2016)

Changed paths: M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py

Log Message: ----------- Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it)

Commit: 8f978b8957f0cbc7e5d78ca3f3bce9e87e6e8f76 https://github.com/galaxyproject/galaxy/commit/8f978b8957f0cbc7e5d78ca3f3bce... Author: Martin Cech cech.marten@gmail.com Date: 2016-07-26 (Tue, 26 Jul 2016)

Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py

Log Message: ----------- Merge pull request #2662 from jmchilton/backport_2253

[16.04] Backport #2253 as requested by Eagle Eyes

Commit: 5d8d932425c879177c40a008a5a2ef3e45020b73 https://github.com/galaxyproject/galaxy/commit/5d8d932425c879177c40a008a5a2e... Author: Daniel Blankenberg dan.blankenberg@gmail.com Date: 2016-07-27 (Wed, 27 Jul 2016)

Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample

Log Message: ----------- Add hg38 to main for ucsc_build_sites.txt.sample

(cherry picked from commit 04b7d11f053e66b14232440e6ff534a62ff26666)

Commit: e4ca3bf80fcab185e8ea3502926563707b047236 https://github.com/galaxyproject/galaxy/commit/e4ca3bf80fcab185e8ea350292656... Author: Enis Afgan afgane@gmail.com Date: 2016-07-28 (Thu, 28 Jul 2016)

Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample

Log Message: ----------- Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04

[16.04] Add hg38 to main for ucsc_build_sites.txt.sample

Commit: c096be04bd53c8184a4c5880c99abe02649e7570 https://github.com/galaxyproject/galaxy/commit/c096be04bd53c8184a4c5880c99ab... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-07-28 (Thu, 28 Jul 2016)

Log Message: ----------- Merge branch 'release_16.04' into dev

Compare: https://github.com/galaxyproject/galaxy/compare/fdbaf437c9ba...c096be04bd53