November 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 9aaafd: Merge pull request #7044 from nsoranzo/release_18....
by GitHub 25 Nov '18

25 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9aaafd8aea1930af02aeebc6b78f03164779ee7c https://github.com/galaxyproject/galaxy/commit/9aaafd8aea1930af02aeebc6b78f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-24 (Sat, 24 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Merge pull request #7044 from nsoranzo/release_18.09_fix/mulled_container_default_channels [18.09] Backport #7038 Commit: 03acc98576085039ab1363b8248369ca646a031d https://github.com/galaxyproject/galaxy/commit/03acc98576085039ab1363b82483… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-25 (Sun, 25 Nov 2018) Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/12dbbb81a7c7...03acc9857608 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 59afe0: fix error when building images where conda channel...
by GitHub 24 Nov '18

24 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 59afe04523b8b00623b92458b4eb275f31401a19 https://github.com/galaxyproject/galaxy/commit/59afe04523b8b00623b92458b4eb… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- fix error when building images where conda channels is passed as a string instead of a list Commit: 5255a0bf20dea411dbc4c1b9b05e757f2e554df1 https://github.com/galaxyproject/galaxy/commit/5255a0bf20dea411dbc4c1b9b05e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Fix ``involucro_auto_init`` default value Commit: 9aaafd8aea1930af02aeebc6b78f03164779ee7c https://github.com/galaxyproject/galaxy/commit/9aaafd8aea1930af02aeebc6b78f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-24 (Sat, 24 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Merge pull request #7044 from nsoranzo/release_18.09_fix/mulled_container_default_channels [18.09] Backport #7038 Compare: https://github.com/galaxyproject/galaxy/compare/4ab4a190fe89...9aaafd8aea19 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 7474ee: fix error when building images where conda channel...
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7474eeadf6375b90fd66bb7545970fd2eb05afe8 https://github.com/galaxyproject/galaxy/commit/7474eeadf6375b90fd66bb754597… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- fix error when building images where conda channels is passed as a string instead of a list Commit: 12dbbb81a7c76b5de0d195f25f0a7b46992db9e0 https://github.com/galaxyproject/galaxy/commit/12dbbb81a7c76b5de0d195f25f0a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-23 (Fri, 23 Nov 2018) Log Message: ----------- Merge pull request #7036 from scholtalbers/fix/mulled_container_default_channels Fix error when building images Compare: https://github.com/galaxyproject/galaxy/compare/dcfbedaa53dd...12dbbb81a7c7 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 59afe0: fix error when building images where conda channel...
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59afe04523b8b00623b92458b4eb275f31401a19 https://github.com/galaxyproject/galaxy/commit/59afe04523b8b00623b92458b4eb… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- fix error when building images where conda channels is passed as a string instead of a list Commit: 5255a0bf20dea411dbc4c1b9b05e757f2e554df1 https://github.com/galaxyproject/galaxy/commit/5255a0bf20dea411dbc4c1b9b05e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-22 (Thu, 22 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Fix ``involucro_auto_init`` default value Commit: dcfbedaa53ddc488b2ac74a63c8bae5a3d206abc https://github.com/galaxyproject/galaxy/commit/dcfbedaa53ddc488b2ac74a63c8b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py Log Message: ----------- Merge pull request #7038 from nsoranzo/release_18.09_fix/mulled_container_default_channels [18.09] Fix error when building images Compare: https://github.com/galaxyproject/galaxy/compare/90076617651b...dcfbedaa53dd **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 992ea5: Pass through ``--daemon`` option to gunicorn
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 992ea5e4b957bb0723d7c8702f26bce8f50d5a05 https://github.com/galaxyproject/galaxy/commit/992ea5e4b957bb0723d7c8702f26… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Pass through ``--daemon`` option to gunicorn Documented at http://docs.gunicorn.org/en/stable/settings.html#daemon Commit: 4ab4a190fe89ecf410ccef269ecb59d985da5804 https://github.com/galaxyproject/galaxy/commit/4ab4a190fe89ecf410ccef269ecb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7042 from nsoranzo/release_18.09_gunicorn_daemon [18.09] Pass through ``--daemon`` option to gunicorn Commit: 90076617651b8159fc75bfeefff2ab5db85cab59 https://github.com/galaxyproject/galaxy/commit/90076617651b8159fc75bfeefff2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8470e9129693...90076617651b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 992ea5: Pass through ``--daemon`` option to gunicorn
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 992ea5e4b957bb0723d7c8702f26bce8f50d5a05 https://github.com/galaxyproject/galaxy/commit/992ea5e4b957bb0723d7c8702f26… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Pass through ``--daemon`` option to gunicorn Documented at http://docs.gunicorn.org/en/stable/settings.html#daemon Commit: 4ab4a190fe89ecf410ccef269ecb59d985da5804 https://github.com/galaxyproject/galaxy/commit/4ab4a190fe89ecf410ccef269ecb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7042 from nsoranzo/release_18.09_gunicorn_daemon [18.09] Pass through ``--daemon`` option to gunicorn Commit: f2c9baf2c54b4f6983887149bb5a9dc01a501c1c https://github.com/galaxyproject/galaxy/commit/f2c9baf2c54b4f6983887149bb5a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge branch 'release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/1ae8eb577db9...f2c9baf2c54b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 992ea5: Pass through ``--daemon`` option to gunicorn
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 992ea5e4b957bb0723d7c8702f26bce8f50d5a05 https://github.com/galaxyproject/galaxy/commit/992ea5e4b957bb0723d7c8702f26… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Pass through ``--daemon`` option to gunicorn Documented at http://docs.gunicorn.org/en/stable/settings.html#daemon Commit: 4ab4a190fe89ecf410ccef269ecb59d985da5804 https://github.com/galaxyproject/galaxy/commit/4ab4a190fe89ecf410ccef269ecb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7042 from nsoranzo/release_18.09_gunicorn_daemon [18.09] Pass through ``--daemon`` option to gunicorn Compare: https://github.com/galaxyproject/galaxy/compare/a1277b0e43b2...4ab4a190fe89 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/ansible-galaxy] 640012: Make safe for --check
by GitHub 23 Nov '18

23 Nov '18

Branch: refs/heads/make-check-safe Home: https://github.com/galaxyproject/ansible-galaxy Commit: 640012f0d7883e011d41e085fdbaedfdeb7d1fae https://github.com/galaxyproject/ansible-galaxy/commit/640012f0d7883e011d41… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M tasks/clone.yml Log Message: ----------- Make safe for --check **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] f04342: workflows api call made public
by GitHub 21 Nov '18

21 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f04342541d3b43adacf8b9f194069e72dc77ec61 https://github.com/galaxyproject/galaxy/commit/f04342541d3b43adacf8b9f19406… Author: Frederik Coppens <frederik.coppens(a)psb.vib-ugent.be> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- workflows api call made public Commit: a94d22a7b3767217cbc90fda118f1e27ded1962c https://github.com/galaxyproject/galaxy/commit/a94d22a7b3767217cbc90fda118f… Author: Frederik Coppens <frederik.coppens(a)psb.vib-ugent.be> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- published workflows accessible through API endpoint Commit: 983f490f9e2928a0abcdd74086952db3043ac1bf https://github.com/galaxyproject/galaxy/commit/983f490f9e2928a0abcdd7408695… Author: Frederik Coppens <frederik.coppens(a)psb.vib-ugent.be> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- show_published only defaults to True when not logged in Commit: 45345533fb6495a109c49b6fe058f1a26609fe15 https://github.com/galaxyproject/galaxy/commit/45345533fb6495a109c49b6fe058… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-21 (Wed, 21 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test cases for public WF access to published workflows. Commit: 8470e91296931ea9d23f4b655a4a2be7d1d51b4c https://github.com/galaxyproject/galaxy/commit/8470e91296931ea9d23f4b655a4a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-21 (Wed, 21 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #7020 from frederikcoppens/public_api_wf Expose published workflows through API Compare: https://github.com/galaxyproject/galaxy/compare/c7bd5c794b3c...8470e9129693 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] 63d0a4: Remove downtime banner
by GitHub 20 Nov '18

20 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 63d0a4e022ae19201fce2db1fee1699d2d51e1eb https://github.com/galaxyproject/usegalaxy-playbook/commit/63d0a4e022ae1920… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove downtime banner **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0