galaxy-commits November 2018

galaxy-commits@lists.galaxyproject.org

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113 discussions

[galaxyproject/galaxy] 9a9b81: add datatype sniff button in edit dataset attribut...
by GitHub 30 Nov '18

30 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9a9b815d8fc9810600668ca358f72e0130e37d8f https://github.com/galaxyproject/galaxy/commit/9a9b815d8fc9810600668ca358f7… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- add datatype sniff button in edit dataset attributes page Commit: 170ed2a8c2a4d324ceac6fabf2a115d6eb801c16 https://github.com/galaxyproject/galaxy/commit/170ed2a8c2a4d324ceac6fabf2a1… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- fix style and wording Commit: 4ff3c95e38d1c62a5d1b85994e2dde909a2f7e38 https://github.com/galaxyproject/galaxy/commit/4ff3c95e38d1c62a5d1b85994e2d… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-11-19 (Mon, 19 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- fix a typo error Commit: 030cf02fc8009cf412a763863756de4b79beba77 https://github.com/galaxyproject/galaxy/commit/030cf02fc8009cf412a763863756… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-30 (Fri, 30 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #7018 from qiagu/join1 Add datatype sniff button to edit dataset attributes page Compare: https://github.com/galaxyproject/galaxy/compare/8c8fc364e1ee...030cf02fc800 **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.

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[galaxyproject/galaxy] 4cde6b: Escape dataset names in job submission success mes...
by GitHub 30 Nov '18

30 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4cde6b9b814acae02393c9fc6b432506cb9c429d https://github.com/galaxyproject/galaxy/commit/4cde6b9b814acae02393c9fc6b43… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Escape dataset names in job submission success message Commit: 8c8fc364e1ee9c1b91f266c13867d27c6f7cca80 https://github.com/galaxyproject/galaxy/commit/8c8fc364e1ee9c1b91f266c13867… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-30 (Fri, 30 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #7062 from guerler/escape_select2 Escape dataset names in job submission success message Compare: https://github.com/galaxyproject/galaxy/compare/4e1618e754f6...8c8fc364e1ee **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.

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[galaxyproject/galaxy] 2a3b22: Update galaxy.yml.sample and galaxy_options.rst
by GitHub 30 Nov '18

30 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2a3b22cf497055a1afc578a1f7aead35f51a0ba2 https://github.com/galaxyproject/galaxy/commit/2a3b22cf497055a1afc578a1f7ae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-30 (Fri, 30 Nov 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- Update galaxy.yml.sample and galaxy_options.rst with `make config-rebuild` . Follow-up on https://github.com/galaxyproject/galaxy/pull/6776 . Commit: 4e1618e754f6bc9b28cbd2fc1dc06c2288b1239f https://github.com/galaxyproject/galaxy/commit/4e1618e754f6bc9b28cbd2fc1dc0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-30 (Fri, 30 Nov 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- Merge pull request #7064 from nsoranzo/make_config-rebuild Update ``galaxy.yml.sample`` and ``galaxy_options.rst`` Compare: https://github.com/galaxyproject/galaxy/compare/7183a17efc7c...4e1618e754f6 **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.

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[galaxyproject/galaxy] 6fa0c8: add new item to the help menu
by GitHub 30 Nov '18

30 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6fa0c8f932831fe91db492de09a2bb4b48621738 https://github.com/galaxyproject/galaxy/commit/6fa0c8f932831fe91db492de09a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- add new item to the help menu Commit: 72f5d1a35f0a854a242c0854f670ab82045e95a9 https://github.com/galaxyproject/galaxy/commit/72f5d1a35f0a854a242c0854f670… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7054 from martenson/help-menu-item-rel [18.09] add new item to the help menu Commit: 247fd018105ae8d08e7eeb89b5f92dfbe6b8548c https://github.com/galaxyproject/galaxy/commit/247fd018105ae8d08e7eeb89b5f9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M static/style/blue/base.css Log Message: ----------- make the transition non-instrusive Commit: d3679e2541045f25e6007efbaed5d9d11f91a8c4 https://github.com/galaxyproject/galaxy/commit/d3679e2541045f25e6007efbaed5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-30 (Fri, 30 Nov 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- revert the changes to css, probably remnant from working on dev Commit: 51afe15f86c0f67e2e51fd0c67ba950a424f0983 https://github.com/galaxyproject/galaxy/commit/51afe15f86c0f67e2e51fd0c67ba… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-30 (Fri, 30 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7061 from martenson/help-menu-item-rel [18.09] make the menu transition non-instrusive Commit: 7183a17efc7cfb598c376eaf0d391efb6848e27d https://github.com/galaxyproject/galaxy/commit/7183a17efc7cfb598c376eaf0d39… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-30 (Fri, 30 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2376d7f2fd57...7183a17efc7c **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.

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[galaxyproject/galaxy] 247fd0: make the transition non-instrusive
by GitHub 30 Nov '18

30 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 247fd018105ae8d08e7eeb89b5f92dfbe6b8548c https://github.com/galaxyproject/galaxy/commit/247fd018105ae8d08e7eeb89b5f9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M static/style/blue/base.css Log Message: ----------- make the transition non-instrusive Commit: d3679e2541045f25e6007efbaed5d9d11f91a8c4 https://github.com/galaxyproject/galaxy/commit/d3679e2541045f25e6007efbaed5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-30 (Fri, 30 Nov 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- revert the changes to css, probably remnant from working on dev Commit: 51afe15f86c0f67e2e51fd0c67ba950a424f0983 https://github.com/galaxyproject/galaxy/commit/51afe15f86c0f67e2e51fd0c67ba… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-30 (Fri, 30 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7061 from martenson/help-menu-item-rel [18.09] make the menu transition non-instrusive Compare: https://github.com/galaxyproject/galaxy/compare/72f5d1a35f0a...51afe15f86c0 **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.

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[galaxyproject/infrastructure-playbook] 5d758f: Proxy Biostar archive in S3 from Athena
by GitHub 29 Nov '18

29 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5d758fb276a8e9d12126155ff8d7d01ad0f5dfae https://github.com/galaxyproject/infrastructure-playbook/commit/5d758fb276a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M env/common/files/ssl/athena.galaxyproject.org_cert.pem M env/common/group_vars/sslservers/vault.yml M env/galaxy/host_vars/athena.galaxyproject.org/vars.yml A env/galaxy/templates/nginx/biostar.j2 Log Message: ----------- Proxy Biostar archive in S3 from Athena **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] 8e9e3b: Started moved from biostar to help.galaxyproject.o...
by GitHub 29 Nov '18

29 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8e9e3b9ba1e1fdfda667625460ae8a772a4d1e3f https://github.com/galaxyproject/usegalaxy-playbook/commit/8e9e3b9ba1e1fdfd… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R env/common/files/galaxy/static/welcome_img/GalaxyBiostar.png R env/common/files/galaxy/static/welcome_img/GalaxyBiostarHelp.png A env/common/files/galaxy/static/welcome_img/galaxy-help.png M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Started moved from biostar to help.galaxyproject.org Commit: 5300cb8a0408afc534149c5b912adb46c4def928 https://github.com/galaxyproject/usegalaxy-playbook/commit/5300cb8a0408afc5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: R env/common/files/galaxy/static/welcome_img/GalaxyBiostar.png R env/common/files/galaxy/static/welcome_img/GalaxyBiostarHelp.png A env/common/files/galaxy/static/welcome_img/galaxy-help.png M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Merge pull request #180 from galaxyproject/biostar-to-discourse Started moved from biostar to help.galaxyproject.org Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/75d65c6b2b44...… **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] 75d65c: remove biostar configuration from Test
by GitHub 29 Nov '18

29 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 75d65c6b2b44421c1d81e6b51cfc9a39a46fd7cd https://github.com/galaxyproject/usegalaxy-playbook/commit/75d65c6b2b44421c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- remove biostar configuration from Test **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] 6fa0c8: add new item to the help menu
by GitHub 29 Nov '18

29 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 6fa0c8f932831fe91db492de09a2bb4b48621738 https://github.com/galaxyproject/galaxy/commit/6fa0c8f932831fe91db492de09a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- add new item to the help menu Commit: 72f5d1a35f0a854a242c0854f670ab82045e95a9 https://github.com/galaxyproject/galaxy/commit/72f5d1a35f0a854a242c0854f670… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #7054 from martenson/help-menu-item-rel [18.09] add new item to the help menu Compare: https://github.com/galaxyproject/galaxy/compare/2620367a5a40...72f5d1a35f0a **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] 8e9e3b: Started moved from biostar to help.galaxyproject.o...
by GitHub 28 Nov '18

28 Nov '18

Branch: refs/heads/biostar-to-discourse Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8e9e3b9ba1e1fdfda667625460ae8a772a4d1e3f https://github.com/galaxyproject/usegalaxy-playbook/commit/8e9e3b9ba1e1fdfd… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: R env/common/files/galaxy/static/welcome_img/GalaxyBiostar.png R env/common/files/galaxy/static/welcome_img/GalaxyBiostarHelp.png A env/common/files/galaxy/static/welcome_img/galaxy-help.png M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Started moved from biostar to help.galaxyproject.org **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.

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galaxy-commits November 2018