February 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6733c3: [17.01] Restore logging statement missing when res...
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 6733c36318bacce0bbf33a8d266f6a08de3ba019 https://github.com/galaxyproject/galaxy/commit/6733c36318bacce0bbf33a8d266f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- [17.01] Restore logging statement missing when resolve_all is used. Broken in #3391. Commit: 49ef352235f7c998e79ca5423fab9725ea28d8be https://github.com/galaxyproject/galaxy/commit/49ef352235f7c998e79ca5423fab… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3646 from jmchilton/resolve_all_logging [17.01] Restore logging statement missing when resolve_all is used. Compare: https://github.com/galaxyproject/galaxy/compare/29f8b54c9a8a...49ef352235f7

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[galaxyproject/infrastructure-playbook] 8bd3cb: Add more Jetstream instances
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8bd3cb6a9872050eda133a4f15b72929afa13b8e https://github.com/galaxyproject/infrastructure-playbook/commit/8bd3cb6a987… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M jetstreamiuenv/inventory M jetstreamtaccenv/inventory Log Message: ----------- Add more Jetstream instances

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[galaxyproject/galaxy] 9abe8a: Allow composite datatypes of type auto_primary_fil...
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9abe8a7b91d969a5b3af2bc026911dcde8656e24 https://github.com/galaxyproject/galaxy/commit/9abe8a7b91d969a5b3af2bc02691… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/__init__.py Log Message: ----------- Allow composite datatypes of type auto_primary_file to automatically generate primary datatype for standard (non-upload) jobs when the tool does not already create the file. Commit: badf49daa54a660a032ac22b2e4b7c84c92284e1 https://github.com/galaxyproject/galaxy/commit/badf49daa54a660a032ac22b2e4b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #3643 from blankenberg/composite-datatype-auto-gen Allow composite datatypes of type auto_primary_file to automatically generate dataset Compare: https://github.com/galaxyproject/galaxy/compare/cdb15f63925e...badf49daa54a

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[galaxyproject/infrastructure-playbook] 522690: Fix collection of hostlist
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 522690cf66c298c1af532072874c797be0b86aaa https://github.com/galaxyproject/infrastructure-playbook/commit/522690cf66c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M roles/slurm/tasks/main.yml Log Message: ----------- Fix collection of hostlist

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[galaxyproject/usegalaxy-playbook] 643964: Add missing branch name option to galaxy.yml playb...
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 64396455a66d94d3ce41b748e0a47396813a3f8a https://github.com/galaxyproject/usegalaxy-playbook/commit/64396455a66d94d3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M galaxy.yml Log Message: ----------- Add missing branch name option to galaxy.yml playbook Commit: 16147fb88ec5a2cf3c4add53d954ccd1bd263f18 https://github.com/galaxyproject/usegalaxy-playbook/commit/16147fb88ec5a2cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M production/galaxy_version.yml M production/group_vars/all.yml Log Message: ----------- Upgrade Main to the usegalaxy branch Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/452187f73626...…

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[galaxyproject/galaxy] 277c4e: Pull build_sites out of datatypes conf.
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 277c4ed20bdf8d38e6b98dc5e8d4d1d350ea4d2f https://github.com/galaxyproject/galaxy/commit/277c4ed20bdf8d38e6b98dc5e8d4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: A config/build_sites.yml.sample M config/datatypes_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M scripts/common_startup.sh Log Message: ----------- Pull build_sites out of datatypes conf. So deployers may modify these paths and stil use the default datatypes config. This should speed up set_metadata also since each of these config files won't be loaded as part of that.

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[galaxyproject/infrastructure-playbook] 7d2345: Add new Jetstream instances at TACC
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 7d2345abf4846ff23b1e901b3ed7167343d827fc https://github.com/galaxyproject/infrastructure-playbook/commit/7d2345abf48… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M jetstreamtaccenv/inventory Log Message: ----------- Add new Jetstream instances at TACC

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[galaxyproject/galaxy] f7a14e: Use `command -v` rather than `which` when determin...
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: f7a14e1c90270f557d52fda196400653b0b9d09f https://github.com/galaxyproject/galaxy/commit/f7a14e1c90270f557d52fda19640… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Use `command -v` rather than `which` when determining Galaxy Python for external set metadata. Commit: 29f8b54c9a8a975473ecbee96992ec400fd138b5 https://github.com/galaxyproject/galaxy/commit/29f8b54c9a8a975473ecbee96992… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Merge pull request #3638 from natefoo/use-version-not-which [17.01] Use `command -v` rather than `which` when determining Galaxy Python for external set metadata Compare: https://github.com/galaxyproject/galaxy/compare/62475c50a039...29f8b54c9a8a

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[galaxyproject/usegalaxy-playbook] 452187: update subrepo
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 452187f73626149d1776f34b135e9fc5853881aa https://github.com/galaxyproject/usegalaxy-playbook/commit/452187f73626149d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M common_roles Log Message: ----------- update subrepo

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[galaxyproject/galaxy] 305f46: Fix inability to access API key for users
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 305f461d45ab010c10fa6061cd7d248e354a9967 https://github.com/galaxyproject/galaxy/commit/305f461d45ab010c10fa6061cd7d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix inability to access API key for users Commit: 62475c50a03927aa2461543c227c60909adff332 https://github.com/galaxyproject/galaxy/commit/62475c50a03927aa2461543c227c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3640 from erasche/fix-api-access-external [17.01] Fix inability to access API key for users Compare: https://github.com/galaxyproject/galaxy/compare/caf57c6f3e21...62475c50a039

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