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

[galaxyproject/galaxy] a310b0: Fix minor typo in rule builder.
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: a310b0a121e19c126b2c5bdaa093b2f2bb056c5a https://github.com/galaxyproject/galaxy/commit/a310b0a121e19c126b2c5bdaa093… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix minor typo in rule builder. Commit: 48de2ecf21d5b68596e308b2a37696eff54e37d0 https://github.com/galaxyproject/galaxy/commit/48de2ecf21d5b68596e308b2a376… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- client-format Commit: bf51c8352648b4a56a4a162deee4c37ee8e551db https://github.com/galaxyproject/galaxy/commit/bf51c8352648b4a56a4a162deee4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6140 from dannon/minor_typo [18.05] Minor typo in rule builder Compare: https://github.com/galaxyproject/galaxy/compare/3d6443b58bfa...bf51c8352648 **NOTE:** This service 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] 69dce8: Use bootstrap-vue for Sharing.mako; convert alert,...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69dce8d38a5d151a4239d577def65eb88cc46f0f https://github.com/galaxyproject/galaxy/commit/69dce8d38a5d151a4239d577def6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Use bootstrap-vue for Sharing.mako; convert alert, drop unnecessary component style Commit: 824b5721b051cc490180d9204fbb61ef7a94ab48 https://github.com/galaxyproject/galaxy/commit/824b5721b051cc490180d9204fbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/managers/sharable.py Log Message: ----------- Fix bug where if username was null (which is allowed), the sharable manager blew up. Commit: 351709a6ba8cf07ac66e3ea7357f32c6d4c8c996 https://github.com/galaxyproject/galaxy/commit/351709a6ba8cf07ac66e3ea7357f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Swap to bsvue-buttons and table. If we really want this a table, we should restyle it. I think we can probably just kill the table, now that I've converted it. Commit: e52802f8fd0e349b8f222cbf56fd1d9ca4f63491 https://github.com/galaxyproject/galaxy/commit/e52802f8fd0e349b8f222cbf56fd… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/managers/sharable.py Log Message: ----------- Merge pull request #6132 from dannon/bsvue-sharing Sharing.vue bootstrapping and a bugfix Compare: https://github.com/galaxyproject/galaxy/compare/6a1057e95f5e...e52802f8fd0e **NOTE:** This service 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] 616c1b: Add a text label length limit for select2's used i...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 616c1b971a01d7a7cf2967e1fea225c4466d13eb https://github.com/galaxyproject/galaxy/commit/616c1b971a01d7a7cf2967e1fea2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-12 (Sat, 12 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Add a text label length limit for select2's used in the upload dialog Reduce limit to a 100 characters Match encapsulated values in title string Commit: 8be2da03b52e819d5e4e4ac76dea983f4f0c2448 https://github.com/galaxyproject/galaxy/commit/8be2da03b52e819d5e4e4ac76dea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Improve dialog message while waiting for rule builder job. Commit: 788ed8aa43296537c6439d0fea7a5446ffe15da0 https://github.com/galaxyproject/galaxy/commit/788ed8aa43296537c6439d0fea7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Improve data initialization of rule builder for long term support. A mistake was made in the rush to rule-builder-all-the-stuffs - libraries, hdas, and FTP all initialized a different set of columns from the data (which is probably fine) but with no indication this was happening in the underlying rules (which is definitely not fine). To understand why this was a mistake and see why in the long term this hurts reproducibility, take loading rules for HDAs from the history panel as an example. In the initial implementation it would pre-initialize two columns - one for "hid" and one for "name" - any rules that were generated from there would start with an implicit assumption of two columns. This is a problem because if someone saves some rules and we (Galaxy developers) decide later on that name tag should be in the initial list but HID doesn't make sense and make that change - we basically are breaking all existing rules to support a very logical change in behavior. Likewise, Galaxy produces a hash with last modified date and size for each FTP entry - this is data we have and could stick in the rule builder by default - but if we change that over time existing FTP rules will break. It would be much more sustainable to instead include the initial column generation information in the initial rules generated - so that each of these modalities start in reality with an empty table and the initial set of rules describe what metadata to pull initial columns from. This way if you save a set of rules it will include the initial column choices, and if they are pasted in at some later point where columns are picked differently - the rules will still work because you are replacing the initial column definitions. The initial rules implementation didn't have this concept of loading columns from metadata - but this was added to support loading existing identifiers as part of the "Apply Rules to Existing Collection" tool. This commit extends that idea to do the same thing (but with different columns) when loading data from HDAs, FTP, and data libraries. Commit: c5ab87ee5909e0871fb62fcb2e82cdaecf5f8166 https://github.com/galaxyproject/galaxy/commit/c5ab87ee5909e0871fb62fcb2e82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Fix repeated additions of the separator, define vars. Commit: 9789aa7d637f8e0a1de558f01ef90a136f7e79a3 https://github.com/galaxyproject/galaxy/commit/9789aa7d637f8e0a1de558f01ef9… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Merge pull request #26 from dannon/max_select2_length Fix a minor bug, a little bit of cleanup. Commit: b0d730fa76cf8392a19cea5fe08a72aab2fccc2a https://github.com/galaxyproject/galaxy/commit/b0d730fa76cf8392a19cea5fe08a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Merge pull request #6130 from guerler/max_select2_length [18.05] Limit select2 text label length to 100 characters Commit: e5ea32465a64fed1acfa63b7385272a6f9ccee15 https://github.com/galaxyproject/galaxy/commit/e5ea32465a64fed1acfa63b73852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- More validation for rule builder. - Require a URL or FTP column for raw pasted data. - Require list identifiers if creating collections. - Require name in more scenerios that require a name. Commit: 5c036bc2647799c70b11b2a4e4ce0fae8d103cdc https://github.com/galaxyproject/galaxy/commit/5c036bc2647799c70b11b2a4e4ce… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6133 from jmchilton/rule_fixes_7 [18.05] Improve dialog message while waiting for rule builder job. Commit: 076e1ddaecd4f2744346c503b0108d8189f35bd1 https://github.com/galaxyproject/galaxy/commit/076e1ddaecd4f2744346c503b010… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6136 from jmchilton/rule_fixes_9 [18.05] More validation for rule builder. Commit: 3d6443b58bfa0200cf775b569c542be326476493 https://github.com/galaxyproject/galaxy/commit/3d6443b58bfa0200cf775b569c54… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Merge pull request #6134 from jmchilton/rule_fixes_8 Improve data initialization of rule builder for long term support. Commit: 6a1057e95f5e46cbd676aaf6dbfe3a4df706d9c3 https://github.com/galaxyproject/galaxy/commit/6a1057e95f5e46cbd676aaf6dbfe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7077851e9813...6a1057e95f5e **NOTE:** This service 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] 788ed8: Improve data initialization of rule builder for lo...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 788ed8aa43296537c6439d0fea7a5446ffe15da0 https://github.com/galaxyproject/galaxy/commit/788ed8aa43296537c6439d0fea7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Improve data initialization of rule builder for long term support. A mistake was made in the rush to rule-builder-all-the-stuffs - libraries, hdas, and FTP all initialized a different set of columns from the data (which is probably fine) but with no indication this was happening in the underlying rules (which is definitely not fine). To understand why this was a mistake and see why in the long term this hurts reproducibility, take loading rules for HDAs from the history panel as an example. In the initial implementation it would pre-initialize two columns - one for "hid" and one for "name" - any rules that were generated from there would start with an implicit assumption of two columns. This is a problem because if someone saves some rules and we (Galaxy developers) decide later on that name tag should be in the initial list but HID doesn't make sense and make that change - we basically are breaking all existing rules to support a very logical change in behavior. Likewise, Galaxy produces a hash with last modified date and size for each FTP entry - this is data we have and could stick in the rule builder by default - but if we change that over time existing FTP rules will break. It would be much more sustainable to instead include the initial column generation information in the initial rules generated - so that each of these modalities start in reality with an empty table and the initial set of rules describe what metadata to pull initial columns from. This way if you save a set of rules it will include the initial column choices, and if they are pasted in at some later point where columns are picked differently - the rules will still work because you are replacing the initial column definitions. The initial rules implementation didn't have this concept of loading columns from metadata - but this was added to support loading existing identifiers as part of the "Apply Rules to Existing Collection" tool. This commit extends that idea to do the same thing (but with different columns) when loading data from HDAs, FTP, and data libraries. Commit: 3d6443b58bfa0200cf775b569c542be326476493 https://github.com/galaxyproject/galaxy/commit/3d6443b58bfa0200cf775b569c54… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Merge pull request #6134 from jmchilton/rule_fixes_8 Improve data initialization of rule builder for long term support. Compare: https://github.com/galaxyproject/galaxy/compare/076e1ddaecd4...3d6443b58bfa **NOTE:** This service 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] e5ea32: More validation for rule builder.
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: e5ea32465a64fed1acfa63b7385272a6f9ccee15 https://github.com/galaxyproject/galaxy/commit/e5ea32465a64fed1acfa63b73852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- More validation for rule builder. - Require a URL or FTP column for raw pasted data. - Require list identifiers if creating collections. - Require name in more scenerios that require a name. Commit: 076e1ddaecd4f2744346c503b0108d8189f35bd1 https://github.com/galaxyproject/galaxy/commit/076e1ddaecd4f2744346c503b010… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6136 from jmchilton/rule_fixes_9 [18.05] More validation for rule builder. Compare: https://github.com/galaxyproject/galaxy/compare/5c036bc26477...076e1ddaecd4 **NOTE:** This service 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] 1940be: Add a script to prune ZFS snapshots from westvlete...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1940bef1f7b65f380a5c9dd695b245ee2a34e5bd https://github.com/galaxyproject/infrastructure-playbook/commit/1940bef1f7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M common_roles A env/common/_inc_handlers.yml M env/galaxy/_inc_baseenv.yml A env/galaxy/_inc_handlers.yml A env/galaxy/files/system/prunesnaps A env/galaxy/files/westvleteren/prunesnaps.conf M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml Log Message: ----------- Add a script to prune ZFS snapshots from westvleteren. Testing, so not running from cron just yet **NOTE:** This service 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] b77fa9: Clean cgroups every 5 minutes until I can figure o...
by GitHub 14 May '18

14 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b77fa95f1a7f946616cc4b9270abf0a0805d19bd https://github.com/galaxyproject/infrastructure-playbook/commit/b77fa95f1a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: A env/tacc/files/system/cleancgroups.py M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Clean cgroups every 5 minutes until I can figure out why they're not being removed by slurm **NOTE:** This service 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] 8be2da: Improve dialog message while waiting for rule buil...
by GitHub 14 May '18

14 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 8be2da03b52e819d5e4e4ac76dea983f4f0c2448 https://github.com/galaxyproject/galaxy/commit/8be2da03b52e819d5e4e4ac76dea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Improve dialog message while waiting for rule builder job. Commit: 5c036bc2647799c70b11b2a4e4ce0fae8d103cdc https://github.com/galaxyproject/galaxy/commit/5c036bc2647799c70b11b2a4e4ce… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6133 from jmchilton/rule_fixes_7 [18.05] Improve dialog message while waiting for rule builder job. Compare: https://github.com/galaxyproject/galaxy/compare/b0d730fa76cf...5c036bc26477 **NOTE:** This service 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] 5d7fc1: Use from_work_dir in CONVERTER_fasta_to_fai
by GitHub 14 May '18

14 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5d7fc1a379a6a21fb5d401fb726837530a348c50 https://github.com/galaxyproject/galaxy/commit/5d7fc1a379a6a21fb5d401fb7268… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- Use from_work_dir in CONVERTER_fasta_to_fai Commit: 7077851e981312ca3ee0e47627e55496d8b8427a https://github.com/galaxyproject/galaxy/commit/7077851e981312ca3ee0e47627e5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- Merge pull request #6135 from nsoranzo/fasta_to_fai_from_work_dir Use from_work_dir in CONVERTER_fasta_to_fai Compare: https://github.com/galaxyproject/galaxy/compare/1fc06c22f884...7077851e9813 **NOTE:** This service 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] 616c1b: Add a text label length limit for select2's used i...
by GitHub 14 May '18

14 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 616c1b971a01d7a7cf2967e1fea225c4466d13eb https://github.com/galaxyproject/galaxy/commit/616c1b971a01d7a7cf2967e1fea2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-12 (Sat, 12 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Add a text label length limit for select2's used in the upload dialog Reduce limit to a 100 characters Match encapsulated values in title string Commit: c5ab87ee5909e0871fb62fcb2e82cdaecf5f8166 https://github.com/galaxyproject/galaxy/commit/c5ab87ee5909e0871fb62fcb2e82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Fix repeated additions of the separator, define vars. Commit: 9789aa7d637f8e0a1de558f01ef90a136f7e79a3 https://github.com/galaxyproject/galaxy/commit/9789aa7d637f8e0a1de558f01ef9… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Merge pull request #26 from dannon/max_select2_length Fix a minor bug, a little bit of cleanup. Commit: b0d730fa76cf8392a19cea5fe08a72aab2fccc2a https://github.com/galaxyproject/galaxy/commit/b0d730fa76cf8392a19cea5fe08a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Merge pull request #6130 from guerler/max_select2_length [18.05] Limit select2 text label length to 100 characters Compare: https://github.com/galaxyproject/galaxy/compare/19c5c7395e2d...b0d730fa76cf **NOTE:** This service 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