galaxy-commits May 2018

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217 discussions

[galaxyproject/galaxy] fcde0d: Avoid overlapping change handlers
by GitHub 22 May '18

22 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fcde0d669f3e65bf92f05dc517fe550d017c86c4 https://github.com/galaxyproject/galaxy/commit/fcde0d669f3e65bf92f05dc517fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Avoid overlapping change handlers Commit: 49c824cf01d3b03d7041dc9a2ebe438471dd27e0 https://github.com/galaxyproject/galaxy/commit/49c824cf01d3b03d7041dc9a2ebe… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Merge pull request #6185 from guerler/fix_repeat_inputs [18.05] Fix repeated inputs Commit: 4d38c25c9f746370d9070dfc3d00a488a3b9e27f https://github.com/galaxyproject/galaxy/commit/4d38c25c9f746370d9070dfc3d00… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Right align button menu popup Commit: 2fe24e470d9e555674685006475c9f5cbe00f0c3 https://github.com/galaxyproject/galaxy/commit/2fe24e470d9e555674685006475c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #6188 from guerler/fix_popup_right [18.05] Right align button menu popup Commit: b931356ef3ea6a2b99add6ed180fa81c64b59632 https://github.com/galaxyproject/galaxy/commit/b931356ef3ea6a2b99add6ed180f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Fix sphinx. Commit: 440f17875f6b5ce36147ee1e830162e40c0c0d48 https://github.com/galaxyproject/galaxy/commit/440f17875f6b5ce36147ee1e8301… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Merge pull request #6191 from jmchilton/fix_sphinx [18.05] Lock dependency on Sphinx to <1.7. Commit: d47e5f25e44405c8bbf5a5fa7a5d62ef709c5e8b https://github.com/galaxyproject/galaxy/commit/d47e5f25e44405c8bbf5a5fa7a5d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a992637de17d...d47e5f25e444 **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] b93135: Fix sphinx.
by GitHub 22 May '18

22 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: b931356ef3ea6a2b99add6ed180fa81c64b59632 https://github.com/galaxyproject/galaxy/commit/b931356ef3ea6a2b99add6ed180f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Fix sphinx. Commit: 440f17875f6b5ce36147ee1e830162e40c0c0d48 https://github.com/galaxyproject/galaxy/commit/440f17875f6b5ce36147ee1e8301… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Merge pull request #6191 from jmchilton/fix_sphinx [18.05] Lock dependency on Sphinx to <1.7. Compare: https://github.com/galaxyproject/galaxy/compare/2fe24e470d9e...440f17875f6b **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/usegalaxy-playbook] aa34f8: Increase memory for GIEs to 2GB
by GitHub 22 May '18

22 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aa34f8162afa0fc1089bb5d478c5b7801f100ce4 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa34f8162afa0fc1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/main/group_vars/galaxywebservers.yml Log Message: ----------- Increase memory for GIEs to 2GB **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] 691bbf: Restart docker nightly on swarm managers because I...
by GitHub 22 May '18

22 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 691bbfbf5db0cee5d7c5c25cbb15029d5c504ee0 https://github.com/galaxyproject/infrastructure-playbook/commit/691bbfbf5db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/galaxy/group_vars/dockerswarmmanagers/vars.yml M env/galaxy/playbook.yml Log Message: ----------- Restart docker nightly on swarm managers because I hate swarm **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] 4d38c2: Right align button menu popup
by GitHub 22 May '18

22 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 4d38c25c9f746370d9070dfc3d00a488a3b9e27f https://github.com/galaxyproject/galaxy/commit/4d38c25c9f746370d9070dfc3d00… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Right align button menu popup Commit: 2fe24e470d9e555674685006475c9f5cbe00f0c3 https://github.com/galaxyproject/galaxy/commit/2fe24e470d9e555674685006475c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #6188 from guerler/fix_popup_right [18.05] Right align button menu popup Compare: https://github.com/galaxyproject/galaxy/compare/49c824cf01d3...2fe24e470d9e **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] fcde0d: Avoid overlapping change handlers
by GitHub 22 May '18

22 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: fcde0d669f3e65bf92f05dc517fe550d017c86c4 https://github.com/galaxyproject/galaxy/commit/fcde0d669f3e65bf92f05dc517fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Avoid overlapping change handlers Commit: 49c824cf01d3b03d7041dc9a2ebe438471dd27e0 https://github.com/galaxyproject/galaxy/commit/49c824cf01d3b03d7041dc9a2ebe… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Merge pull request #6185 from guerler/fix_repeat_inputs [18.05] Fix repeated inputs Compare: https://github.com/galaxyproject/galaxy/compare/805854aa6b16...49c824cf01d3 **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] c25343: Fix append() for ANY_COLLECTION_TYPE type descript...
by GitHub 22 May '18

22 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c253436b4a7c646910bdc1f8ce9c2f01fe43f1ff https://github.com/galaxyproject/galaxy/commit/c253436b4a7c646910bdc1f8ce9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix append() for ANY_COLLECTION_TYPE type description in WF editor. Append means take a collection type and extend it by the current type - so appending to list to paired -> list:paired for instance. ANY_COLLECTION_TYPE is a representation of incomplete information - it means this type description might be any kind of collection type (the way we use "input" to mean any kind of datatype in the editor). This is really a second order approximation of what a correct solution would be - a first order approximation would somehow represent the result of append being at least of "depth" specified (list:* or *:list instead of * for instance). A not approximation would be to do that but use ANY_COLLECTION_TYPE much less frequently by capturing type_source information and propagating it throughout the workflow properly. But these are harder things to do, this incorrect fix will allow many valid workflows to be editted that currently cannot be so I think it is good. "Fixes" #5205. Commit: f8fc8232a68dd1b0693ff9b007734cfa087cccdf https://github.com/galaxyproject/galaxy/commit/f8fc8232a68dd1b0693ff9b00773… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-19 (Sat, 19 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #6178 from jmchilton/fix_append_for_any_collection_Type [18.05] Fix append() for ANY_COLLECTION_TYPE type description in WF editor. Commit: 872dbfb3c42ec36ffe3c452e164e0dcc2545c3cb https://github.com/galaxyproject/galaxy/commit/872dbfb3c42ec36ffe3c452e164e… Author: Ubuntu <ubuntu(a)ip-172-31-23-81.ec2.internal> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- adding idat Commit: 258c4a4d8fddacba64a5cc7ac634910a4839b371 https://github.com/galaxyproject/galaxy/commit/258c4a4d8fddacba64a5cc7ac634… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6179 from kpbioteam/idat [18.05] add idat datatype Commit: f56150468984cc96e37fe52cefd33499e5f422b4 https://github.com/galaxyproject/galaxy/commit/f56150468984cc96e37fe52cefd3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Rev subprocess32 dependency - that older version is not compatible with manylinux. https://github.com/google/python-subprocess32/issues/12 Commit: f07ba172418bdea209481b56b60980d2c9906823 https://github.com/galaxyproject/galaxy/commit/f07ba172418bdea209481b56b609… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- extraneous self Commit: 92ebf285088c744cef588a05b941ca6adf7848ee https://github.com/galaxyproject/galaxy/commit/92ebf285088c744cef588a05b941… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #6184 from erasche/gdpr [18.05] extraneous self causing bug reporter to fail Commit: 805854aa6b16eb2b68b6ab5f94b92e84342c2f9e https://github.com/galaxyproject/galaxy/commit/805854aa6b16eb2b68b6ab5f94b9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6183 from jmchilton/subprocess32_rev [18.05] Rev subprocess32 dependency - that older version is not compatible with manylinux. Commit: a992637de17d36b9b821dabc5342f636c530e4bc https://github.com/galaxyproject/galaxy/commit/a992637de17d36b9b821dabc5342… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/datatypes_conf.xml.sample M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/errors.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d0cb1d6f3c1c...a992637de17d **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] f56150: Rev subprocess32 dependency - that older version i...
by GitHub 21 May '18

21 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f56150468984cc96e37fe52cefd33499e5f422b4 https://github.com/galaxyproject/galaxy/commit/f56150468984cc96e37fe52cefd3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Rev subprocess32 dependency - that older version is not compatible with manylinux. https://github.com/google/python-subprocess32/issues/12 Commit: 805854aa6b16eb2b68b6ab5f94b92e84342c2f9e https://github.com/galaxyproject/galaxy/commit/805854aa6b16eb2b68b6ab5f94b9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6183 from jmchilton/subprocess32_rev [18.05] Rev subprocess32 dependency - that older version is not compatible with manylinux. Compare: https://github.com/galaxyproject/galaxy/compare/92ebf285088c...805854aa6b16 **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/usegalaxy-playbook] e2dd20: Increase memory for collection column join
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e2dd20a092d32ecec553cfe25dc5e36f33c999aa https://github.com/galaxyproject/usegalaxy-playbook/commit/e2dd20a092d32ece… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Increase memory for collection column join **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] 98dd77: Switch galaxy06/stats.galaxyproject.org to use sta...
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 98dd777605efab54589964d1021e88ba42267b51 https://github.com/galaxyproject/infrastructure-playbook/commit/98dd777605e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/tacc/group_vars/statsservers/vars.yml Log Message: ----------- Switch galaxy06/stats.galaxyproject.org to use standard config/data/service layout for influxdb and grafana **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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galaxy-commits May 2018