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

[galaxyproject/usegalaxy-playbook] 1ac321: raise sloreq threshold from 1 to 3
by GitHub 10 May '18

10 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1ac321f78dc7339ccce5d3965b65249fe15c609d https://github.com/galaxyproject/usegalaxy-playbook/commit/1ac321f78dc7339c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- raise sloreq threshold from 1 to 3 Commit: a831aea94a006a4f716491f7e4ed22db36410ab4 https://github.com/galaxyproject/usegalaxy-playbook/commit/a831aea94a006a4f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Merge pull request #121 from galaxyproject/sloreq raise sloreq threshold from 1 to 3 Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/e8488ecdc4ac...… **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] a1c58a: When JobWrapper.get_destination_configuration() is...
by GitHub 10 May '18

10 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1c58a708829d79859426ecb7c39b5c5f69ad735 https://github.com/galaxyproject/galaxy/commit/a1c58a708829d79859426ecb7c39… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/model/__init__.py Log Message: ----------- When JobWrapper.get_destination_configuration() is called, check the JobDestination params in addition to the destination_params persisted on the Job and the app configuration Commit: eeb1dae5b71200ffe9f2056b2a7fd8ed560033c1 https://github.com/galaxyproject/galaxy/commit/eeb1dae5b71200ffe9f2056b2a7f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Make JobWrapper/TaskWrapper's dataset_path_rewriter a property Commit: 2dd301d0b5c0fa69b372b4d5a8a029b385c4e3c3 https://github.com/galaxyproject/galaxy/commit/2dd301d0b5c0fa69b372b4d5a8a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix error due to name mangling. Commit: cb8f8322c85e90e846c31f9370ca8930504b5298 https://github.com/galaxyproject/galaxy/commit/cb8f8322c85e90e846c31f9370ca… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6087 from natefoo/job-dest-config-fix Fix JobWrapper.get_destination_configuration() so that it actually checks the JobDestination params Compare: https://github.com/galaxyproject/galaxy/compare/cd723e4f8efe...cb8f8322c85e **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] e8488e: Unbreak Pulsar on Test until per-dest outputs_to_w...
by GitHub 10 May '18

10 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e8488ecdc4ac4cbb77eb75c164d9994422985228 https://github.com/galaxyproject/usegalaxy-playbook/commit/e8488ecdc4ac4cbb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Unbreak Pulsar on Test until per-dest outputs_to_working_directory fix is in. **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] d3877f: Test mutable config
by GitHub 10 May '18

10 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d3877feed1431cd77848466d7761a367d3faba44 https://github.com/galaxyproject/usegalaxy-playbook/commit/d3877feed1431cd7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Test mutable config Commit: e0a050b3cd14b5f75fd45a77b7e3a4fbddc33b62 https://github.com/galaxyproject/usegalaxy-playbook/commit/e0a050b3cd14b5f7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/all.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Update Test to test singularity_image_dir Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/770f83edec68...… **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] ba1f36: Encode dataset ids when loading trackster visualiz...
by GitHub 10 May '18

10 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: ba1f369e2f1c124ffacd60b329364d79d63ed513 https://github.com/galaxyproject/galaxy/commit/ba1f369e2f1c124ffacd60b32936… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Encode dataset ids when loading trackster visualizations Commit: b6a22584aaed8df8ea3ffc1d1db96c65fe887878 https://github.com/galaxyproject/galaxy/commit/b6a22584aaed8df8ea3ffc1d1db9… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6112 from guerler/fix_hda_access [18.05] Encode dataset ids when loading trackster visualizations Compare: https://github.com/galaxyproject/galaxy/compare/b7f26be45fd0...b6a22584aaed **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] 507a60: Remove duplicate visualization list entries from m...
by GitHub 10 May '18

10 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 507a60a23062fc037b0893fd23b84980c32fd9ef https://github.com/galaxyproject/galaxy/commit/507a60a23062fc037b0893fd23b8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Remove duplicate visualization list entries from masthead Commit: cd723e4f8efe94cd5c6f885c192dc06e97788a1a https://github.com/galaxyproject/galaxy/commit/cd723e4f8efe94cd5c6f885c192d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Merge pull request #6110 from guerler/remove_duplicate_vis_list Remove duplicate visualization list entries from masthead Compare: https://github.com/galaxyproject/galaxy/compare/a4b03d10a96b...cd723e4f8efe **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] eae69c: [18.05] Fix parsing last argument when running fun...
by GitHub 10 May '18

10 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: eae69c26f89aa6b809a3186131f59b32d590bb9e https://github.com/galaxyproject/galaxy/commit/eae69c26f89aa6b809a3186131f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M run_tests.sh Log Message: ----------- [18.05] Fix parsing last argument when running functional tests. Causes Planemo to double test tools. Commit: b7f26be45fd0fa13876cfdfdd37c460b9947474b https://github.com/galaxyproject/galaxy/commit/b7f26be45fd0fa13876cfdfdd37c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #6095 from jmchilton/fix_double_test [18.05] Fix parsing last argument when running functional tests. Compare: https://github.com/galaxyproject/galaxy/compare/fa4d7b49a786...b7f26be45fd0 **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] 182823: Add singularity CVMFS repo
by GitHub 10 May '18

10 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1828236555134caeac33815a9cdf840c5ef7ff95 https://github.com/galaxyproject/infrastructure-playbook/commit/18282365551… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M env/galaxy/group_vars/cvmfsstratum1servers/vars.yml M env/galaxy/group_vars/cvmfsstratum1servers/vault.yml M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vault.yml M roles/cvmfs/defaults/main.yml Log Message: ----------- Add singularity CVMFS repo **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] 0031eb: Respect workflow_building_modes.ENABLED in workflo...
by GitHub 10 May '18

10 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0031eb59beb0c04e602353824e61d0aa735f573b https://github.com/galaxyproject/galaxy/commit/0031eb59beb0c04e602353824e61… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Respect workflow_building_modes.ENABLED in workflow manager's to_dict. Commit: c4a909a66e86f2a60fa4c2b637e817a82143e2b5 https://github.com/galaxyproject/galaxy/commit/c4a909a66e86f2a60fa4c2b637e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Simplify config_form logic for editor's to_dict Commit: fa4d7b49a786e36f85033e953da4c8604f089ec4 https://github.com/galaxyproject/galaxy/commit/fa4d7b49a786e36f85033e953da4… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #6075 from dannon/workflow_building_mode [18.05] Respect workflow_building_modes.ENABLED in workflow manager's to_dict. Commit: a4b03d10a96bf6652711a8ac996c5f048ef8e568 https://github.com/galaxyproject/galaxy/commit/a4b03d10a96bf6652711a8ac996c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/4e6560843127...a4b03d10a96b **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] 0031eb: Respect workflow_building_modes.ENABLED in workflo...
by GitHub 10 May '18

10 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 0031eb59beb0c04e602353824e61d0aa735f573b https://github.com/galaxyproject/galaxy/commit/0031eb59beb0c04e602353824e61… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Respect workflow_building_modes.ENABLED in workflow manager's to_dict. Commit: c4a909a66e86f2a60fa4c2b637e817a82143e2b5 https://github.com/galaxyproject/galaxy/commit/c4a909a66e86f2a60fa4c2b637e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Simplify config_form logic for editor's to_dict Commit: fa4d7b49a786e36f85033e953da4c8604f089ec4 https://github.com/galaxyproject/galaxy/commit/fa4d7b49a786e36f85033e953da4… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #6075 from dannon/workflow_building_mode [18.05] Respect workflow_building_modes.ENABLED in workflow manager's to_dict. Compare: https://github.com/galaxyproject/galaxy/compare/ef7d90a3dec1...fa4d7b49a786 **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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