galaxy-commits May 2017

galaxy-commits@lists.galaxyproject.org

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135 discussions

[galaxyproject/usegalaxy-playbook] 9e45cf: Jupyter updates for Test
by GitHub 02 May '17

02 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9e45cf23ef9cbc87f398b5d7b302de0bd7c814b1 https://github.com/galaxyproject/usegalaxy-playbook/commit/9e45cf23ef9cbc87… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Jupyter updates for Test

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[galaxyproject/usegalaxy-playbook] 9fdad3: Override walltime in dynamic rules
by GitHub 02 May '17

02 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9fdad33717d819c7370b5d2c8413170f30fba1e7 https://github.com/galaxyproject/usegalaxy-playbook/commit/9fdad33717d819c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Override walltime in dynamic rules

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[galaxyproject/usegalaxy-playbook] e765f7: Allow overriding the walltime on a per-tool basis
by GitHub 02 May '17

02 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e765f7f020a92885a9fb74cc125bd9ddf53cdc23 https://github.com/galaxyproject/usegalaxy-playbook/commit/e765f7f020a92885… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Allow overriding the walltime on a per-tool basis

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[galaxyproject/infrastructure-playbook] 58ff4f: Change ownership of data.galaxyproject.org repo to...
by GitHub 02 May '17

02 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 58ff4fc05465dd554f2306b7de9b8a7b2abc44c6 https://github.com/galaxyproject/infrastructure-playbook/commit/58ff4fc0546… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M galaxyenv/host_vars/cvmfs0-psu0.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml Log Message: ----------- Change ownership of data.galaxyproject.org repo to g2test Commit: 7002b8f547c4015d201321c335909bc977e0f544 https://github.com/galaxyproject/infrastructure-playbook/commit/7002b8f547c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M galaxyenv/playbook.yml M galaxyenv/secret_group_vars/all.yml A galaxyenv/secret_group_vars/dockerswarmmanagers.yml Log Message: ----------- Swarm manager user setup Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/50f9fef379…

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[galaxyproject/galaxy]
by GitHub 02 May '17

02 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] f3aee7: More careful inspection of fixes for MAF tools req...
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3aee70c9547c349061cbf22760d604f5f30c821 https://github.com/galaxyproject/galaxy/commit/f3aee70c9547c349061cbf22760d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- More careful inspection of fixes for MAF tools requiring Galaxy. Add two tools that required the hack, and remove one tool that doesn't seem to require it. Tracked in comment on #3934. Commit: 60e00088c8b27c04734c7f7adb3cdae6a9a9580f https://github.com/galaxyproject/galaxy/commit/60e00088c8b27c04734c7f7adb3c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix edge case for workflow mapping handling when tools not available. Fixes #3960. Commit: 3fcd78564630fae9c4670cfbe198572f94f688c0 https://github.com/galaxyproject/galaxy/commit/3fcd78564630fae9c4670cfbe198… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #3962 from jmchilton/workflow_editor_mapping_test [17.01] Fix edge case for workflow mapping handling when tools not available. Commit: de46a0edba4c49bafa061a08fc49c5d7f72cbd30 https://github.com/galaxyproject/galaxy/commit/de46a0edba4c49bafa061a08fc49… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3935 from jmchilton/more_maf_fixes [17.01] More careful inspection of fixes for MAF tools requiring Galaxy. Commit: 06d0e4fce57fa29e6d7fb02c455b77f6855f783c https://github.com/galaxyproject/galaxy/commit/06d0e4fce57fa29e6d7fb02c455b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/tools/__init__.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ecf634a619e9...06d0e4fce57f

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[galaxyproject/usegalaxy-playbook] f92005: Override walltime in dynamic rules
by GitHub 02 May '17

02 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f92005350152572a09c9a7071e4aa0f9afd1c5d1 https://github.com/galaxyproject/usegalaxy-playbook/commit/f92005350152572a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Override walltime in dynamic rules

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[galaxyproject/galaxy] d224be: Implicitly set use_volumes = False if using Docker...
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d224bedd3992e413363f345d64488e13d63518fe https://github.com/galaxyproject/galaxy/commit/d224bedd3992e413363f345d6448… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Implicitly set use_volumes = False if using Docker swarm Commit: ecf634a619e93ffe98b5b785e3de10125940adce https://github.com/galaxyproject/galaxy/commit/ecf634a619e93ffe98b5b785e3de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #4006 from natefoo/implicit-use-volumes Implicitly set use_volumes = False if using Docker swarm Compare: https://github.com/galaxyproject/galaxy/compare/afc4fbcc3829...ecf634a619e9

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[galaxyproject/galaxy] 4b3a36: Update Jupyter image to 17.05
by GitHub 02 May '17

02 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b3a361a887d02e1944fd092b1c3a84b7da13f95 https://github.com/galaxyproject/galaxy/commit/4b3a361a887d02e1944fd092b1c3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Update Jupyter image to 17.05 Commit: afc4fbcc38292c90641dcac737fd08ad0c253201 https://github.com/galaxyproject/galaxy/commit/afc4fbcc38292c90641dcac737fd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Merge pull request #4007 from natefoo/jupyer-17.05 Update Jupyter image to 17.05 Compare: https://github.com/galaxyproject/galaxy/compare/0680a29a7992...afc4fbcc3829

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[galaxyproject/usegalaxy-playbook] dfe930: Update Test
by GitHub 02 May '17

02 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dfe930e2290d6cbfb91bd8cb182595b4491fd7cf https://github.com/galaxyproject/usegalaxy-playbook/commit/dfe930e2290d6cbf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/interactive_environments/plugins/.ansible_ie_role_current_version M env/test/files/interactive_environments/plugins/common/templates/ie.mako M env/test/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js M env/test/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako M env/test/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M env/test/files/interactive_environments/plugins/jupyter/templates/jupyter.mako M env/test/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample M env/test/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M env/test/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M env/test/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version M env/test/files/interactive_environments/proxy/package.json Log Message: ----------- Update Test

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galaxy-commits May 2017