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

[galaxyproject/usegalaxy-playbook] 7dcb6b: Update Main
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7dcb6bd67a7685fde19831a77bbdae1d04dcd70f https://github.com/galaxyproject/usegalaxy-playbook/commit/7dcb6bd67a7685fd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main **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] f07ba1: extraneous self
by GitHub 21 May '18

21 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/258c4a4d8fdd...92ebf285088c **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] 197a16: Add X11 runtime libs for Conda R
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 197a16c2ade835b66a0344783f7fd90de4393a63 https://github.com/galaxyproject/infrastructure-playbook/commit/197a16c2ade… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Add X11 runtime libs for Conda R **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] a49d14: Reenable UnkillableStepTimeout as disabling it was...
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a49d1483782a64e390c30f5b2977beccc4687171 https://github.com/galaxyproject/infrastructure-playbook/commit/a49d1483782… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Reenable UnkillableStepTimeout as disabling it was causing lots of node drain **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] 872dbf: adding idat
by GitHub 21 May '18

21 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/f8fc8232a68d...258c4a4d8fdd **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 19 May '18

19 May '18

Branch: refs/heads/release_18.05 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. Compare: https://github.com/galaxyproject/galaxy/compare/afc8d0abd81b...f8fc8232a68d **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] f4e824: Updated lastz to version 1.3.2
by GitHub 18 May '18

18 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f4e8242ca584f37198ead277fd1fe92c5c50d128 https://github.com/galaxyproject/usegalaxy-playbook/commit/f4e8242ca584f371… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated lastz to version 1.3.2 **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] 2fef59: Fix upload file selector value resetting
by GitHub 18 May '18

18 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2fef59aa46c06aebe42c1f075c2d84a86fc11a30 https://github.com/galaxyproject/galaxy/commit/2fef59aa46c06aebe42c1f075c2d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix upload file selector value resetting Fix Commit: d0cb1d6f3c1c49d690a1b7279c7c1ef30df3593b https://github.com/galaxyproject/galaxy/commit/d0cb1d6f3c1c49d690a1b7279c7c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6168 from guerler/fix_upload_selector [18.05] Fix upload file selector value resetting Compare: https://github.com/galaxyproject/galaxy/compare/d714dfb2fa36...d0cb1d6f3c1c **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] 240ad3: Fix dataset access validation when attempting job ...
by GitHub 18 May '18

18 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 240ad36e20f34f1083b7d148340d4fadd72f8884 https://github.com/galaxyproject/galaxy/commit/240ad36e20f34f1083b7d148340d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix dataset access validation when attempting job reruns Commit: c8ecb0b38dd172a73e0bd5ee86ce80fe83a1007e https://github.com/galaxyproject/galaxy/commit/c8ecb0b38dd172a73e0bd5ee86ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Add sample commentary to the stub in config manage, xref a88e19064a38415d867f4c118dd6938d8e368632 Commit: 6a30fe14f1ac018b424b38cba69827ddbfff186a https://github.com/galaxyproject/galaxy/commit/6a30fe14f1ac018b424b38cba698… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Config rebuild Commit: c6ce1342df0155fa848f551df41f01c016fcc98f https://github.com/galaxyproject/galaxy/commit/c6ce1342df0155fa848f551df41f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- More standard spacing in additional config comments just added. Commit: bd4f562005e26d56b5e4c9476748fb14f0fed242 https://github.com/galaxyproject/galaxy/commit/bd4f562005e26d56b5e4c9476748… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #6170 from mvdbeek/backport_6169 [18.01] Backport #6169 Fix dataset access validation when attempting job reruns Commit: 5489504e9794f31e26adc901f5612fcfb7d4a91d https://github.com/galaxyproject/galaxy/commit/5489504e9794f31e26adc901f561… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: afc8d0abd81b56b0eb1797e9acca2e574976939b https://github.com/galaxyproject/galaxy/commit/afc8d0abd81b56b0eb1797e9acca… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- Merge pull request #6172 from nsoranzo/release_18.05_backport_virtualenv_config [18.05] Restore config comment Commit: d714dfb2fa36c4ee9c067c85782eff4ae1d86f08 https://github.com/galaxyproject/galaxy/commit/d714dfb2fa36c4ee9c067c85782e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-18 (Fri, 18 May 2018) Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/41e12f0b9d17...d714dfb2fa36 **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] c8ecb0: Add sample commentary to the stub in config manage...
by GitHub 18 May '18

18 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c8ecb0b38dd172a73e0bd5ee86ce80fe83a1007e https://github.com/galaxyproject/galaxy/commit/c8ecb0b38dd172a73e0bd5ee86ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Add sample commentary to the stub in config manage, xref a88e19064a38415d867f4c118dd6938d8e368632 Commit: 6a30fe14f1ac018b424b38cba69827ddbfff186a https://github.com/galaxyproject/galaxy/commit/6a30fe14f1ac018b424b38cba698… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Config rebuild Commit: c6ce1342df0155fa848f551df41f01c016fcc98f https://github.com/galaxyproject/galaxy/commit/c6ce1342df0155fa848f551df41f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- More standard spacing in additional config comments just added. Commit: afc8d0abd81b56b0eb1797e9acca2e574976939b https://github.com/galaxyproject/galaxy/commit/afc8d0abd81b56b0eb1797e9acca… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py Log Message: ----------- Merge pull request #6172 from nsoranzo/release_18.05_backport_virtualenv_config [18.05] Restore config comment Compare: https://github.com/galaxyproject/galaxy/compare/5489504e9794...afc8d0abd81b **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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