galaxy-commits May 2016

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[galaxyproject/galaxy] 0e511b: Remove assumed parameter value from error message
by GitHub 23 May '16

23 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0e511b78a4d515f5b8c454e96683b2dc76b1f8df https://github.com/galaxyproject/galaxy/commit/0e511b78a4d515f5b8c454e96683… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove assumed parameter value from error message Commit: 4a2e67036127d8088b96f7f767907f76f3c9012d https://github.com/galaxyproject/galaxy/commit/4a2e67036127d8088b96f7f76790… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Avoid empty strings when converting values to display text Commit: bfca29a98a1fe26131bcf3b181e0b65ad82130c6 https://github.com/galaxyproject/galaxy/commit/bfca29a98a1fe26131bcf3b181e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add proper validation error for missing single values in data tool parameters Commit: 5918b054130484ec253c0d18b3901141b8c903e3 https://github.com/galaxyproject/galaxy/commit/5918b054130484ec253c0d18b390… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Show default value in error warning only if its different than the initial value Commit: 04e34f346f19fc29c8dd0d0532b676bc782f0a3e https://github.com/galaxyproject/galaxy/commit/04e34f346f19fc29c8dd0d0532b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2391 from guerler/revise_tool_framework_001 Align and improve validation errors and value to text conversions Compare: https://github.com/galaxyproject/galaxy/compare/4461f2458840...04e34f346f19

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[galaxyproject/galaxy] 0c4601: Fix the installed conda version to 3.19.3.
by GitHub 23 May '16

23 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c4601aaecedf61e77aef4eea9e777829fa5a40d https://github.com/galaxyproject/galaxy/commit/0c4601aaecedf61e77aef4eea9e7… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-21 (Sat, 21 May 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix the installed conda version to 3.19.3. Commit: 4461f24588400ec861a6159437f0c7c7dc4697d0 https://github.com/galaxyproject/galaxy/commit/4461f24588400ec861a6159437f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2394 from bgruening/fix_conda_install Fix the installed conda version to 3.19.3. Compare: https://github.com/galaxyproject/galaxy/compare/389fa8ad7da8...4461f2458840

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[galaxyproject/usegalaxy-playbook] 0494df: Updated slide rotation: May 20 GCC2016 deadlines r...
by GitHub 21 May '16

21 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0494dff450343c21e35f1c797b0adc791ce53f1e https://github.com/galaxyproject/usegalaxy-playbook/commit/0494dff450343c21… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-05-21 (Sat, 21 May 2016) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016June4Deadlines.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation: May 20 GCC2016 deadlines replaced with June 4 deadlines.

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[galaxyproject/galaxy]
by GitHub 20 May '16

20 May '16

Branch: refs/heads/fix_pep8 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/usegalaxy-playbook] bfd90d: Update Pulsar role
by GitHub 20 May '16

20 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bfd90d94d8c005b8c67e35a0bc8b3cfdd56fa62f https://github.com/galaxyproject/usegalaxy-playbook/commit/bfd90d94d8c005b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M roles/galaxyprojectdotorg.pulsar/README.md M roles/galaxyprojectdotorg.pulsar/defaults/main.yml M roles/galaxyprojectdotorg.pulsar/meta/.galaxy_install_info M roles/galaxyprojectdotorg.pulsar/tasks/main.yml M roles/galaxyprojectdotorg.pulsar/templates/server.ini.j2 Log Message: ----------- Update Pulsar role Commit: cf361e8432ce45b4a0be9cabf66472b397982c70 https://github.com/galaxyproject/usegalaxy-playbook/commit/cf361e8432ce45b4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M galaxy.yml M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M production/group_vars/pulsarservers.yml A production/host_vars/jetstream-tacc0.galaxyproject.org.yml M production/host_vars/login5.stampede.tacc.utexas.edu.yml M production/inventory M pulsar.yml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M stage/group_vars/pulsarservers.yml M stage/host_vars/greenfield.psc.xsede.org.yml A stage/host_vars/jetstream-tacc0.galaxyproject.org.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml M stage/inventory M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Switch Test and Main from embedded to remote (RESTful) Pulsar on Jetstream for performance reasons. A few things of note: - /cvmfs/<instance>.galaxyproject.org/config/datatypes_conf.xml is currently created by hand. - Supervisor is configured by hand to run Pulsar on jetstream-tacc0 - jetstream-iu is draining old embedded jobs. No jobs will go to IU until it is set up with remote pulsar and the job config (and dynamic rule) is updated. - Need to set up SSL for Pulsar Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/2f7c3b4a6747...…

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[galaxyproject/galaxy] 3de0c1: Fixes pep8 issues from #2386
by GitHub 20 May '16

20 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3de0c16091141aaed22e3a4773877aaa1040a900 https://github.com/galaxyproject/galaxy/commit/3de0c16091141aaed22e3a477387… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fixes pep8 issues from #2386 Commit: 389fa8ad7da8a82dd3bacdf52a7914aee889a112 https://github.com/galaxyproject/galaxy/commit/389fa8ad7da8a82dd3bacdf52a79… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2392 from galaxyproject/fix_pep8 Fixes pep8 issues from #2386 Compare: https://github.com/galaxyproject/galaxy/compare/a743e530d09f...389fa8ad7da8

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[galaxyproject/galaxy] 3de0c1: Fixes pep8 issues from #2386
by GitHub 20 May '16

20 May '16

Branch: refs/heads/fix_pep8 Home: https://github.com/galaxyproject/galaxy Commit: 3de0c16091141aaed22e3a4773877aaa1040a900 https://github.com/galaxyproject/galaxy/commit/3de0c16091141aaed22e3a477387… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fixes pep8 issues from #2386

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[galaxyproject/ansible-pulsar]
by GitHub 20 May '16

20 May '16

Branch: refs/tags/0.4.2 Home: https://github.com/galaxyproject/ansible-pulsar

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[galaxyproject/ansible-pulsar] a5759d: Additional configurability, especially for uWSGI
by GitHub 20 May '16

20 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-pulsar Commit: a5759d31a3f49bfc1ee7dc54437c845080231fd0 https://github.com/galaxyproject/ansible-pulsar/commit/a5759d31a3f49bfc1ee7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M README.md M defaults/main.yml M tasks/main.yml M templates/server.ini.j2 Log Message: ----------- Additional configurability, especially for uWSGI

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[galaxyproject/galaxy] 308f74: Ever more informative, explicit, and complete rele...
by GitHub 20 May '16

20 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 308f74a25a5e7d4212f3b5644b312fe5e38139d8 https://github.com/galaxyproject/galaxy/commit/308f74a25a5e7d4212f3b5644b31… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Ever more informative, explicit, and complete release checklist. - Update announcement acitivties to reflect release notes handled by devs in a diffrent, earlier step. - Add example post links for various announcement activities. - Add credential location information for Twitter. - Add branch-time item to update bioblend target testing. - Add item for scheduling a committer priority meeting (as done for this release by @martenson - thanks for taking charge on that!). Commit: a743e530d09fc41b98c2e796ccd37fb27bbe3125 https://github.com/galaxyproject/galaxy/commit/a743e530d09fc41b98c2e796ccd3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2388 from jmchilton/bootstrap_history_somemore Ever more informative, explicit, and complete release checklist. Compare: https://github.com/galaxyproject/galaxy/compare/4f3e0f6d4057...a743e530d09f

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galaxy-commits May 2016