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

[galaxyproject/usegalaxy-playbook] de7ba9: Update mutable configs after bcftools installation...
by GitHub 18 Dec '18

18 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: de7ba90de1575537bfdfb1d914f5d051015bda9d https://github.com/galaxyproject/usegalaxy-playbook/commit/de7ba90de1575537… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update mutable configs after bcftools installation 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.

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[galaxyproject/galaxy] fe349e: Remove __collected_datasets__ from hook dict.
by GitHub 18 Dec '18

18 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fe349ef334f643faf08fe35b4f1da87e82fa1bbf https://github.com/galaxyproject/galaxy/commit/fe349ef334f643faf08fe35b4f1d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Remove __collected_datasets__ from hook dict. Added for Tool subclass hooks in ca8cc1420ef80bd2fef17fa9bb21dbb0714b4a88 but doesn't seem to be used in any tool implementation hooks. Commit: faec3dc0589189ce12522f2466cb62b0c80c8ccf https://github.com/galaxyproject/galaxy/commit/faec3dc0589189ce12522f2466cb… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #7123 from jmchilton/collected_remove Remove unused __collected_datasets__ from tool hook dict. Compare: https://github.com/galaxyproject/galaxy/compare/d7539d07eb42...faec3dc05891 **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] 0fdb89: Fixes state-change animations causing 'block' disp...
by GitHub 17 Dec '18

17 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0fdb89a1b447d33ea0c62c47f56d0a06a1d0d1bf https://github.com/galaxyproject/galaxy/commit/0fdb89a1b447d33ea0c62c47f56d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Fixes state-change animations causing 'block' display appearing in various places due to collection job state fetches. Includes some import/export refactoring and general client cleanup. Commit: d7539d07eb426dbf7176f67434715671ccda63d7 https://github.com/galaxyproject/galaxy/commit/d7539d07eb426dbf7176f6743471… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-12-17 (Mon, 17 Dec 2018) Changed paths: M client/galaxy/scripts/components/GalaxyLoader.vue M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Merge pull request #7122 from dannon/collection_jobstate_animation_fix Fixes state-change animations causing 'block' display Compare: https://github.com/galaxyproject/galaxy/compare/b22b7e58680f...d7539d07eb42 **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] 855ccb: GRT: Rip out all parameters, round file sizes
by GitHub 16 Dec '18

16 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 855ccb12791a649d72598ba2433491bd5d705899 https://github.com/galaxyproject/galaxy/commit/855ccb12791a649d72598ba24334… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-11-23 (Fri, 23 Nov 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- GRT: Rip out all parameters, round file sizes Commit: 480143af57163b416f56566153e55d32b90e195b https://github.com/galaxyproject/galaxy/commit/480143af57163b416f56566153e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Handle extra cruft sent along by facebook login redirects Commit: f8ed3e73253e9ad2b893c14409173f9b504f00cc https://github.com/galaxyproject/galaxy/commit/f8ed3e73253e9ad2b893c1440917… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Client format. Commit: 691fbfe606fba9399f66ffeed916294d3a4e5113 https://github.com/galaxyproject/galaxy/commit/691fbfe606fba9399f66ffeed916… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-12-06 (Thu, 06 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix set_peek method for copied datasets dataset_assoc is the job to ouptut dataset association that references the HDA created by a job. If the HDA is copied the copies need to be updated as well, so here we need to call `set_peek` on dataset, not dataset_assoc.dataset. Broken in f4343d876f13e55e92ca228582b4430dcd01e4aa Thanks for tracking this down @jmchilton! Commit: 0e5c96ef3710612bf1171e7094cf7d5427387ecb https://github.com/galaxyproject/galaxy/commit/0e5c96ef3710612bf1171e7094cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1). Commit: b10cfa43ac547eaecbd996cef7201170a0e0da8c https://github.com/galaxyproject/galaxy/commit/b10cfa43ac547eaecbd996cef720… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Remove unused $GXPIP_VERSION Commit: efe84751a7bf84b2297df7b77b514b8425fe7c70 https://github.com/galaxyproject/galaxy/commit/efe84751a7bf84b2297df7b77b51… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 6db721915fe0565f0ddfb3dcf863cd4ad5c17a57 https://github.com/galaxyproject/galaxy/commit/6db721915fe0565f0ddfb3dcf863… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Merge pull request #7041 from erasche/fix-grt [18.09] GRT: Rip out all parameters, round file sizes Commit: 4df43adae6fb8e5fb7ab3a7d3c029835a88f3f1a https://github.com/galaxyproject/galaxy/commit/4df43adae6fb8e5fb7ab3a7d3c02… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js Log Message: ----------- Merge pull request #7074 from dannon/fix_for_facebook_auth [18.09] Fix welcome on redirect from facebook auth Commit: 7dd7d8a5e99d0d4bb0ad4c317d8e9d29c749136d https://github.com/galaxyproject/galaxy/commit/7dd7d8a5e99d0d4bb0ad4c317d8e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #7078 from mvdbeek/fix_peek_for_running_datasets [18.09] Fix set_peek method for copied datasets Commit: 8f14121518d1298f5a603e8e52ae5c05212e6360 https://github.com/galaxyproject/galaxy/commit/8f14121518d1298f5a603e8e52ae… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 [16.01] Backport #2383 Commit: 87fa60939696fb4ecbf157e124eacd7afe4c9243 https://github.com/galaxyproject/galaxy/commit/87fa60939696fb4ecbf157e124ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: f3c81816db24d7a0b0f3909919c6ca41664fb50d https://github.com/galaxyproject/galaxy/commit/f3c81816db24d7a0b0f3909919c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: a2e70ef67ec9899af50720aac9f3bf16cbc636ac https://github.com/galaxyproject/galaxy/commit/a2e70ef67ec9899af50720aac9f3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 1b30a9a1b98e40befb34eb7c5197610d4eea786f https://github.com/galaxyproject/galaxy/commit/1b30a9a1b98e40befb34eb7c5197… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 06cfb7e206357718e530c9afa6723c205b664927 https://github.com/galaxyproject/galaxy/commit/06cfb7e206357718e530c9afa672… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: fdd9a091f86c312c4995a47dc674814609a5519c https://github.com/galaxyproject/galaxy/commit/fdd9a091f86c312c4995a47dc674… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 6feef2a2801e15a770997a3dd9556ca46d6c2ca5 https://github.com/galaxyproject/galaxy/commit/6feef2a2801e15a770997a3dd955… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: bfc634e41536e53fcf05ba97714c48dc8fbcccf4 https://github.com/galaxyproject/galaxy/commit/bfc634e41536e53fcf05ba97714c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 65ca25ed669f4cea983d86460f614666ba3571d1 https://github.com/galaxyproject/galaxy/commit/65ca25ed669f4cea983d86460f61… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: b22b7e58680fce07ce57440951ec581a74faa463 https://github.com/galaxyproject/galaxy/commit/b22b7e58680fce07ce57440951ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/jobs/__init__.py M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9dcb002505a1...b22b7e58680f **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] 0e5c96: Drop "Galaxy pip" in favor of manylinux1 wheels (w...
by GitHub 16 Dec '18

16 Dec '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 0e5c96ef3710612bf1171e7094cf7d5427387ecb https://github.com/galaxyproject/galaxy/commit/0e5c96ef3710612bf1171e7094cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1). Commit: b10cfa43ac547eaecbd996cef7201170a0e0da8c https://github.com/galaxyproject/galaxy/commit/b10cfa43ac547eaecbd996cef720… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Remove unused $GXPIP_VERSION Commit: efe84751a7bf84b2297df7b77b514b8425fe7c70 https://github.com/galaxyproject/galaxy/commit/efe84751a7bf84b2297df7b77b51… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 8f14121518d1298f5a603e8e52ae5c05212e6360 https://github.com/galaxyproject/galaxy/commit/8f14121518d1298f5a603e8e52ae… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 [16.01] Backport #2383 Commit: 87fa60939696fb4ecbf157e124eacd7afe4c9243 https://github.com/galaxyproject/galaxy/commit/87fa60939696fb4ecbf157e124ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: f3c81816db24d7a0b0f3909919c6ca41664fb50d https://github.com/galaxyproject/galaxy/commit/f3c81816db24d7a0b0f3909919c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: a2e70ef67ec9899af50720aac9f3bf16cbc636ac https://github.com/galaxyproject/galaxy/commit/a2e70ef67ec9899af50720aac9f3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 1b30a9a1b98e40befb34eb7c5197610d4eea786f https://github.com/galaxyproject/galaxy/commit/1b30a9a1b98e40befb34eb7c5197… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 06cfb7e206357718e530c9afa6723c205b664927 https://github.com/galaxyproject/galaxy/commit/06cfb7e206357718e530c9afa672… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: fdd9a091f86c312c4995a47dc674814609a5519c https://github.com/galaxyproject/galaxy/commit/fdd9a091f86c312c4995a47dc674… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 6feef2a2801e15a770997a3dd9556ca46d6c2ca5 https://github.com/galaxyproject/galaxy/commit/6feef2a2801e15a770997a3dd955… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: bfc634e41536e53fcf05ba97714c48dc8fbcccf4 https://github.com/galaxyproject/galaxy/commit/bfc634e41536e53fcf05ba97714c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 65ca25ed669f4cea983d86460f614666ba3571d1 https://github.com/galaxyproject/galaxy/commit/65ca25ed669f4cea983d86460f61… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/7dd7d8a5e99d...65ca25ed669f **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] 0e5c96: Drop "Galaxy pip" in favor of manylinux1 wheels (w...
by GitHub 16 Dec '18

16 Dec '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 0e5c96ef3710612bf1171e7094cf7d5427387ecb https://github.com/galaxyproject/galaxy/commit/0e5c96ef3710612bf1171e7094cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1). Commit: b10cfa43ac547eaecbd996cef7201170a0e0da8c https://github.com/galaxyproject/galaxy/commit/b10cfa43ac547eaecbd996cef720… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Remove unused $GXPIP_VERSION Commit: efe84751a7bf84b2297df7b77b514b8425fe7c70 https://github.com/galaxyproject/galaxy/commit/efe84751a7bf84b2297df7b77b51… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 8f14121518d1298f5a603e8e52ae5c05212e6360 https://github.com/galaxyproject/galaxy/commit/8f14121518d1298f5a603e8e52ae… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 [16.01] Backport #2383 Commit: 87fa60939696fb4ecbf157e124eacd7afe4c9243 https://github.com/galaxyproject/galaxy/commit/87fa60939696fb4ecbf157e124ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: f3c81816db24d7a0b0f3909919c6ca41664fb50d https://github.com/galaxyproject/galaxy/commit/f3c81816db24d7a0b0f3909919c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: a2e70ef67ec9899af50720aac9f3bf16cbc636ac https://github.com/galaxyproject/galaxy/commit/a2e70ef67ec9899af50720aac9f3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 1b30a9a1b98e40befb34eb7c5197610d4eea786f https://github.com/galaxyproject/galaxy/commit/1b30a9a1b98e40befb34eb7c5197… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 06cfb7e206357718e530c9afa6723c205b664927 https://github.com/galaxyproject/galaxy/commit/06cfb7e206357718e530c9afa672… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: fdd9a091f86c312c4995a47dc674814609a5519c https://github.com/galaxyproject/galaxy/commit/fdd9a091f86c312c4995a47dc674… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 6feef2a2801e15a770997a3dd9556ca46d6c2ca5 https://github.com/galaxyproject/galaxy/commit/6feef2a2801e15a770997a3dd955… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: bfc634e41536e53fcf05ba97714c48dc8fbcccf4 https://github.com/galaxyproject/galaxy/commit/bfc634e41536e53fcf05ba97714c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/9a6fddcdca70...bfc634e41536 **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] 0e5c96: Drop "Galaxy pip" in favor of manylinux1 wheels (w...
by GitHub 16 Dec '18

16 Dec '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 0e5c96ef3710612bf1171e7094cf7d5427387ecb https://github.com/galaxyproject/galaxy/commit/0e5c96ef3710612bf1171e7094cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1). Commit: b10cfa43ac547eaecbd996cef7201170a0e0da8c https://github.com/galaxyproject/galaxy/commit/b10cfa43ac547eaecbd996cef720… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Remove unused $GXPIP_VERSION Commit: efe84751a7bf84b2297df7b77b514b8425fe7c70 https://github.com/galaxyproject/galaxy/commit/efe84751a7bf84b2297df7b77b51… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 8f14121518d1298f5a603e8e52ae5c05212e6360 https://github.com/galaxyproject/galaxy/commit/8f14121518d1298f5a603e8e52ae… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 [16.01] Backport #2383 Commit: 87fa60939696fb4ecbf157e124eacd7afe4c9243 https://github.com/galaxyproject/galaxy/commit/87fa60939696fb4ecbf157e124ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: f3c81816db24d7a0b0f3909919c6ca41664fb50d https://github.com/galaxyproject/galaxy/commit/f3c81816db24d7a0b0f3909919c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: a2e70ef67ec9899af50720aac9f3bf16cbc636ac https://github.com/galaxyproject/galaxy/commit/a2e70ef67ec9899af50720aac9f3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 1b30a9a1b98e40befb34eb7c5197610d4eea786f https://github.com/galaxyproject/galaxy/commit/1b30a9a1b98e40befb34eb7c5197… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 06cfb7e206357718e530c9afa6723c205b664927 https://github.com/galaxyproject/galaxy/commit/06cfb7e206357718e530c9afa672… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: fdd9a091f86c312c4995a47dc674814609a5519c https://github.com/galaxyproject/galaxy/commit/fdd9a091f86c312c4995a47dc674… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 6feef2a2801e15a770997a3dd9556ca46d6c2ca5 https://github.com/galaxyproject/galaxy/commit/6feef2a2801e15a770997a3dd955… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/988d308a12f3...6feef2a2801e **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] 0e5c96: Drop "Galaxy pip" in favor of manylinux1 wheels (w...
by GitHub 16 Dec '18

16 Dec '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 0e5c96ef3710612bf1171e7094cf7d5427387ecb https://github.com/galaxyproject/galaxy/commit/0e5c96ef3710612bf1171e7094cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1). Commit: b10cfa43ac547eaecbd996cef7201170a0e0da8c https://github.com/galaxyproject/galaxy/commit/b10cfa43ac547eaecbd996cef720… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Remove unused $GXPIP_VERSION Commit: efe84751a7bf84b2297df7b77b514b8425fe7c70 https://github.com/galaxyproject/galaxy/commit/efe84751a7bf84b2297df7b77b51… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 8f14121518d1298f5a603e8e52ae5c05212e6360 https://github.com/galaxyproject/galaxy/commit/8f14121518d1298f5a603e8e52ae… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 [16.01] Backport #2383 Commit: 87fa60939696fb4ecbf157e124eacd7afe4c9243 https://github.com/galaxyproject/galaxy/commit/87fa60939696fb4ecbf157e124ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: f3c81816db24d7a0b0f3909919c6ca41664fb50d https://github.com/galaxyproject/galaxy/commit/f3c81816db24d7a0b0f3909919c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: a2e70ef67ec9899af50720aac9f3bf16cbc636ac https://github.com/galaxyproject/galaxy/commit/a2e70ef67ec9899af50720aac9f3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 1b30a9a1b98e40befb34eb7c5197610d4eea786f https://github.com/galaxyproject/galaxy/commit/1b30a9a1b98e40befb34eb7c5197… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 06cfb7e206357718e530c9afa6723c205b664927 https://github.com/galaxyproject/galaxy/commit/06cfb7e206357718e530c9afa672… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: fdd9a091f86c312c4995a47dc674814609a5519c https://github.com/galaxyproject/galaxy/commit/fdd9a091f86c312c4995a47dc674… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/40cecf6ff421...fdd9a091f86c **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] 0e5c96: Drop "Galaxy pip" in favor of manylinux1 wheels (w...
by GitHub 16 Dec '18

16 Dec '18

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 0e5c96ef3710612bf1171e7094cf7d5427387ecb https://github.com/galaxyproject/galaxy/commit/0e5c96ef3710612bf1171e7094cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1). Commit: b10cfa43ac547eaecbd996cef7201170a0e0da8c https://github.com/galaxyproject/galaxy/commit/b10cfa43ac547eaecbd996cef720… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Remove unused $GXPIP_VERSION Commit: efe84751a7bf84b2297df7b77b514b8425fe7c70 https://github.com/galaxyproject/galaxy/commit/efe84751a7bf84b2297df7b77b51… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 8f14121518d1298f5a603e8e52ae5c05212e6360 https://github.com/galaxyproject/galaxy/commit/8f14121518d1298f5a603e8e52ae… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 [16.01] Backport #2383 Commit: 87fa60939696fb4ecbf157e124eacd7afe4c9243 https://github.com/galaxyproject/galaxy/commit/87fa60939696fb4ecbf157e124ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: f3c81816db24d7a0b0f3909919c6ca41664fb50d https://github.com/galaxyproject/galaxy/commit/f3c81816db24d7a0b0f3909919c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: a2e70ef67ec9899af50720aac9f3bf16cbc636ac https://github.com/galaxyproject/galaxy/commit/a2e70ef67ec9899af50720aac9f3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 1b30a9a1b98e40befb34eb7c5197610d4eea786f https://github.com/galaxyproject/galaxy/commit/1b30a9a1b98e40befb34eb7c5197… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 06cfb7e206357718e530c9afa6723c205b664927 https://github.com/galaxyproject/galaxy/commit/06cfb7e206357718e530c9afa672… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/c4150d200214...06cfb7e20635 **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] 0e5c96: Drop "Galaxy pip" in favor of manylinux1 wheels (w...
by GitHub 16 Dec '18

16 Dec '18

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 0e5c96ef3710612bf1171e7094cf7d5427387ecb https://github.com/galaxyproject/galaxy/commit/0e5c96ef3710612bf1171e7094cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip >= 8.1). Commit: b10cfa43ac547eaecbd996cef7201170a0e0da8c https://github.com/galaxyproject/galaxy/commit/b10cfa43ac547eaecbd996cef720… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Remove unused $GXPIP_VERSION Commit: efe84751a7bf84b2297df7b77b514b8425fe7c70 https://github.com/galaxyproject/galaxy/commit/efe84751a7bf84b2297df7b77b51… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 8f14121518d1298f5a603e8e52ae5c05212e6360 https://github.com/galaxyproject/galaxy/commit/8f14121518d1298f5a603e8e52ae… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge pull request #7094 from nsoranzo/release_16.01_backport_2383 [16.01] Backport #2383 Commit: 87fa60939696fb4ecbf157e124eacd7afe4c9243 https://github.com/galaxyproject/galaxy/commit/87fa60939696fb4ecbf157e124ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: f3c81816db24d7a0b0f3909919c6ca41664fb50d https://github.com/galaxyproject/galaxy/commit/f3c81816db24d7a0b0f3909919c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: a2e70ef67ec9899af50720aac9f3bf16cbc636ac https://github.com/galaxyproject/galaxy/commit/a2e70ef67ec9899af50720aac9f3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 1b30a9a1b98e40befb34eb7c5197610d4eea786f https://github.com/galaxyproject/galaxy/commit/1b30a9a1b98e40befb34eb7c5197… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-16 (Sun, 16 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/fa7f2a4f5c18...1b30a9a1b98e **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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