Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6d5675f5da1e91aece2df4af5d037072e897185 https://github.com/galaxyproject/galaxy/commit/b6d5675f5da1e91aece2df4af5d03... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-01-15 (Tue, 15 Jan 2019)
Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message: ----------- Update galaxy.yml.sample for prefix config
Commit: ae8bf6f793edda9211b59c68d6c029b9fa74154a https://github.com/galaxyproject/galaxy/commit/ae8bf6f793edda9211b59c68d6c02... Author: John Chilton jmchilton@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)
Changed paths: A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst
Log Message: ----------- Release notes raw.
Commit: b5713ca170cfeb574063a2ec9dca8adbee1f7d74 https://github.com/galaxyproject/galaxy/commit/b5713ca170cfeb574063a2ec9dca8... Author: John Chilton jmchilton@gmail.com Date: 2019-02-05 (Tue, 05 Feb 2019)
Changed paths: M doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst M doc/source/releases/index.rst
Log Message: ----------- Progress on 19.01 release notes...
Commit: 16af73423f2c5a1181b016dcc01955c1c2ab037a https://github.com/galaxyproject/galaxy/commit/16af73423f2c5a1181b016dcc0195... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)
Changed paths: M doc/source/releases/19.01.rst
Log Message: ----------- Update doc/source/releases/19.01.rst
Co-Authored-By: jmchilton jmchilton@gmail.com
Commit: 072b8d73eca68201bcf691c7dc9fa22272433ac3 https://github.com/galaxyproject/galaxy/commit/072b8d73eca68201bcf691c7dc9fa... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)
Changed paths: M doc/source/releases/19.01.rst
Log Message: ----------- Update doc/source/releases/19.01.rst
Co-Authored-By: jmchilton jmchilton@gmail.com
Commit: 2a3555d9d73e4a9f72b003a319698f7e8fb01d3c https://github.com/galaxyproject/galaxy/commit/2a3555d9d73e4a9f72b003a319698... Author: John Chilton jmchilton@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)
Changed paths: M doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst
Log Message: ----------- Better Singularity summary thanks to @mvdbeek.
Commit: 94bcb8d00f3fc8817cdca5ef3ab383e705b950d6 https://github.com/galaxyproject/galaxy/commit/94bcb8d00f3fc8817cdca5ef3ab38... Author: John Chilton jmchilton@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)
Changed paths: M doc/source/releases/19.01.rst
Log Message: ----------- More fixes to 19.01 release notes.
Commit: ca4acf78df6cfc89f76b0f09143d0301aac234b4 https://github.com/galaxyproject/galaxy/commit/ca4acf78df6cfc89f76b0f09143d0... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)
Changed paths: M doc/source/releases/19.01_announce.rst
Log Message: ----------- Sort PR numbers
Small fixes.
Commit: 37a93972d59459ffd50d340d53c5f278b3e15dae https://github.com/galaxyproject/galaxy/commit/37a93972d59459ffd50d340d53c5f... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-02-18 (Mon, 18 Feb 2019)
Changed paths: M doc/source/releases/19.01.rst
Log Message: ----------- Fix PR link
Commit: d72f82de98f464ace59db312fe9db398793c3494 https://github.com/galaxyproject/galaxy/commit/d72f82de98f464ace59db312fe9db... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-19 (Tue, 19 Feb 2019)
Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message: ----------- remove Paste config option, reword URL prefix
Commit: 6d24026ba59fbe3e534067cd8dce76d4e6a2f38f https://github.com/galaxyproject/galaxy/commit/6d24026ba59fbe3e534067cd8dce7... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-02-19 (Tue, 19 Feb 2019)
Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message: ----------- Merge pull request #11 from martenson/fix_galaxy_yml_prefix_comments
remove Paste config option, reword URL prefix
Commit: b4fc7c19a80c38b595cb08f05fd6765a07f95920 https://github.com/galaxyproject/galaxy/commit/b4fc7c19a80c38b595cb08f05fd67... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-02-20 (Wed, 20 Feb 2019)
Changed paths: M lib/galaxy/tools/__init__.py
Log Message: ----------- Report line number mismatch in sort collection tool
Otherwise this would just fail because sorted_elements is undefined. I don't think there can be a HDA without metadata, so I've dropped that check.
Commit: 015ce5cedc21c1a318d6455534f52f8acc3d36ca https://github.com/galaxyproject/galaxy/commit/015ce5cedc21c1a318d6455534f52... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-20 (Wed, 20 Feb 2019)
Changed paths: A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst M doc/source/releases/index.rst
Log Message: ----------- Merge pull request #7308 from jmchilton/19.01_release_notes
[19.01] Release notes for 19.01.
Commit: 648d01685bf26c9dcb5231cc61755d95a4696928 https://github.com/galaxyproject/galaxy/commit/648d01685bf26c9dcb5231cc61755... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-20 (Wed, 20 Feb 2019)
Changed paths: M lib/galaxy/tools/__init__.py
Log Message: ----------- Merge pull request #7390 from mvdbeek/more_useful_error_message
[19.01] Report line number mismatch in sort collection tool
Commit: 8c9c27b7f6bd14581af870b0d38339d90501e464 https://github.com/galaxyproject/galaxy/commit/8c9c27b7f6bd14581af870b0d3833... Author: mvdbeek m.vandenbeek@gmail.com Date: 2019-02-21 (Thu, 21 Feb 2019)
Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst
Log Message: ----------- Drop filter-with from docs / .sample
Commit: 726ad9a0f68d134d7bc2ffa37ad3f369787d19da https://github.com/galaxyproject/galaxy/commit/726ad9a0f68d134d7bc2ffa37ad3f... Author: Dannon Baker dannon.baker@gmail.com Date: 2019-02-21 (Thu, 21 Feb 2019)
Changed paths: M Makefile M scripts/common_startup.sh
Log Message: ----------- Bump yarn's network timeout from 2 minutes to 5 minutes.
Commit: 4ad4fe59be7bbcc1917d3a1e039fa3f3a8367709 https://github.com/galaxyproject/galaxy/commit/4ad4fe59be7bbcc1917d3a1e039fa... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-21 (Thu, 21 Feb 2019)
Changed paths: M Makefile M scripts/common_startup.sh
Log Message: ----------- Merge pull request #7399 from dannon/bump_yarn_network_tolerance
[19.01] Bump yarn network tolerance
Commit: 1a0f067590d8dcd88857e38d58f62b95a467c641 https://github.com/galaxyproject/galaxy/commit/1a0f067590d8dcd88857e38d58f62... Author: Martin Cech marten@bx.psu.edu Date: 2019-02-21 (Thu, 21 Feb 2019)
Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message: ----------- change config schema to reflect removing paste options
Commit: 351c188830793946ce6fa71dfaab95fe3af7cf7a https://github.com/galaxyproject/galaxy/commit/351c188830793946ce6fa71dfaab9... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2019-02-22 (Fri, 22 Feb 2019)
Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml
Log Message: ----------- Remove ``filter-with`` and update ``cookie_path`` options also for Tool Shed and Reports
Commit: a83eb67775442f37b22ff20203b88a234ab11bec https://github.com/galaxyproject/galaxy/commit/a83eb67775442f37b22ff20203b88... Author: Nate Coraor nate@bx.psu.edu Date: 2019-02-22 (Fri, 22 Feb 2019)
Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml
Log Message: ----------- Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions.
Commit: 5fc5b4aaab373d344f6d286e9dab4b2ce78f98eb https://github.com/galaxyproject/galaxy/commit/5fc5b4aaab373d344f6d286e9dab4... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)
Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml
Log Message: ----------- Merge pull request #12 from natefoo/mvdbeek-fix_galaxy_yml_prefix_comments
Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions
Commit: 656b3c2f87a0dfd49284e113d7df6f2b88b43464 https://github.com/galaxyproject/galaxy/commit/656b3c2f87a0dfd49284e113d7df6... Author: John Chilton jmchilton@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message: ----------- Refactor dataset fetching in get/set dataset method in web controller.
Commit: 1529758ecb781a8bcbfe727acad9e7f2209c824b https://github.com/galaxyproject/galaxy/commit/1529758ecb781a8bcbfe727acad9e... Author: John Chilton jmchilton@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message: ----------- Merge branch 'release_18.01' into release_18.05
Commit: 2f973ac7fa7726ff309a8a8893962fbcd58ffded https://github.com/galaxyproject/galaxy/commit/2f973ac7fa7726ff309a8a8893962... Author: John Chilton jmchilton@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message: ----------- Merge branch 'release_18.05' into release_18.09
Commit: 8651e1eea3779233c1dff3c28ae7b4a0c3fb9735 https://github.com/galaxyproject/galaxy/commit/8651e1eea3779233c1dff3c28ae7b... Author: John Chilton jmchilton@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)
Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message: ----------- Merge branch 'release_18.09' into release_19.01
Commit: 9b72f5a880e39d1a3fd99d8aa6b1509f4e8d6ad1 https://github.com/galaxyproject/galaxy/commit/9b72f5a880e39d1a3fd99d8aa6b15... Author: Nicola Soranzo nicola.soranzo@gmail.com Date: 2019-02-22 (Fri, 22 Feb 2019)
Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml
Log Message: ----------- Merge pull request #7216 from mvdbeek/fix_galaxy_yml_prefix_comments
[18.09] Update configuration samples
Commit: 808aa5bef7fb5e0aa24818cc4bd9da647ccd3f01 https://github.com/galaxyproject/galaxy/commit/808aa5bef7fb5e0aa24818cc4bd9d... Author: Nate Coraor nate@bx.psu.edu Date: 2019-02-22 (Fri, 22 Feb 2019)
Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml
Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into release_19.01
Commit: ef8f208002993b4e2051a8851e0bdcad804ee339 https://github.com/galaxyproject/galaxy/commit/ef8f208002993b4e2051a8851e0bd... Author: Nate Coraor nate@bx.psu.edu Date: 2019-02-22 (Fri, 22 Feb 2019)
Changed paths: M Makefile M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst A doc/source/releases/19.01.rst M doc/source/releases/19.01_announce.rst A doc/source/releases/19.05_announce.rst M doc/source/releases/index.rst M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M scripts/common_startup.sh
Log Message: ----------- Merge remote-tracking branch 'upstream/release_19.01' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/830c21d6f5ef...ef8f20800299