December 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] e2e3db: update test to 14d25e9d426ef6fb329c0a04f0c0fdf0bea...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e2e3dba47c943790c1397cea89e5d1c1b794828c https://github.com/galaxyproject/usegalaxy-playbook/commit/e2e3dba47c943790… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update test to 14d25e9d426ef6fb329c0a04f0c0fdf0beabe9bf

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[galaxyproject/galaxy] 87ce6c: Fix for loading workflows that have tool verions /...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87ce6c778ffc9087d589914a5eec640da067c231 https://github.com/galaxyproject/galaxy/commit/87ce6c778ffc9087d589914a5eec… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix for loading workflows that have tool verions / step upgrade messages. Commit: 14d25e9d426ef6fb329c0a04f0c0fdf0beabe9bf https://github.com/galaxyproject/galaxy/commit/14d25e9d426ef6fb329c0a04f0c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1348 from blankenberg/workflow_fix Fix for loading workflows that have tool version / step upgrade messages. Compare: https://github.com/galaxyproject/galaxy/compare/f51ee306b1e8...14d25e9d426e

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[galaxyproject/galaxy] e38e44: If GALAXY_SLOTS is defined in the environment, use...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e38e4449cddc0a6b31ca6f19d849cae1796e22df https://github.com/galaxyproject/galaxy/commit/e38e4449cddc0a6b31ca6f19d849… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- If GALAXY_SLOTS is defined in the environment, use it for the local runner when job destinations haven't been configured. Commit: f51ee306b1e88001f76fd818e495cdbd9db2e10c https://github.com/galaxyproject/galaxy/commit/f51ee306b1e88001f76fd818e495… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- Merge pull request #1346 from dannon/local_slots If GALAXY_SLOTS is defined in the environment, use it for the local r… Compare: https://github.com/galaxyproject/galaxy/compare/191f75407ed9...f51ee306b1e8

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[galaxyproject/usegalaxy-playbook] a597ab: update Test
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a597ab44eb195565f35b4d51bc47e3b886761491 https://github.com/galaxyproject/usegalaxy-playbook/commit/a597ab44eb195565… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update Test

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[galaxyproject/galaxy] f54138: Fix optional parameters
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f54138237dcba721d61af5f692b3195e812a6939 https://github.com/galaxyproject/galaxy/commit/f54138237dcba721d61af5f692b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix optional parameters Commit: 191f75407ed955b3b0836b7503616f664f0d0a73 https://github.com/galaxyproject/galaxy/commit/191f75407ed955b3b0836b750361… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1343 from guerler/fix_validation_000 Fix optional parameters Compare: https://github.com/galaxyproject/galaxy/compare/8480f9187e8c...191f75407ed9

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[galaxyproject/galaxy] 952eb3: Upgrade Paste to 2.0.2
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 952eb34f447772918f8af7f66779c5dfa734424a https://github.com/galaxyproject/galaxy/commit/952eb34f447772918f8af7f66779… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Upgrade Paste to 2.0.2 Commit: 8480f9187e8cae34fc4822ae1d2d8971f3504f5a https://github.com/galaxyproject/galaxy/commit/8480f9187e8cae34fc4822ae1d2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1344 from natefoo/paste2 Upgrade Paste to 2.0.2 Compare: https://github.com/galaxyproject/galaxy/compare/b9cba364982a...8480f9187e8c

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[galaxyproject/galaxy] 9b30b1: Reduce code duplication by reusing get_installed_r...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 9b30b134d6ab93c2a84a856352f32a6713dd49cd https://github.com/galaxyproject/galaxy/commit/9b30b134d6ab93c2a84a856352f3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce code duplication by reusing get_installed_repository() function. Commit: 11eca70db129173ea20aac0040c9645049af189c https://github.com/galaxyproject/galaxy/commit/11eca70db129173ea20aac0040c9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Workaround for issue #1283, which causes the loaded tool to have a StockLineage instead of a ToolShedLineage, thus creating multiple entries for the tool in the panel. Commit: 1b3ee81dbae9375443ea396280c1e418cae84876 https://github.com/galaxyproject/galaxy/commit/1b3ee81dbae9375443ea396280c1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1314 from nsoranzo/release_15.10_tool_load_fixes [15.10] When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Compare: https://github.com/galaxyproject/galaxy/compare/a23e644a9cd7...1b3ee81dbae9

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[galaxyproject/galaxy] 41b77d: Use local versions of node modules instead of syst...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 41b77d0c1352e569d861ed327fd523dd12efffae https://github.com/galaxyproject/galaxy/commit/41b77d0c1352e569d861ed327fd5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M Makefile M client/README.md Log Message: ----------- Use local versions of node modules instead of system-installed, add a 'build-it-all' target for building the whole client. Fix two old typos. Commit: b9cba364982a9fa77fc2952fb803da75ee8d26e2 https://github.com/galaxyproject/galaxy/commit/b9cba364982a9fa77fc2952fb803… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M Makefile M client/README.md Log Message: ----------- Merge pull request #1337 from dannon/makefile_singletarget Simpler build-it-all rule in Makefile Compare: https://github.com/galaxyproject/galaxy/compare/8cc10c98ec45...b9cba364982a

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[galaxyproject/galaxy] f1c364: Don't bother querying on unencoded IDs
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f1c36485c1ecef33667f3c35bad44899233d04f5 https://github.com/galaxyproject/galaxy/commit/f1c36485c1ecef33667f3c35bad4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Don't bother querying on unencoded IDs Commit: 8cc10c98ec4569ccfe1226d4c28a8526abbf3f44 https://github.com/galaxyproject/galaxy/commit/8cc10c98ec4569ccfe1226d4c28a… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #1340 from erasche/id_decoding Don't bother querying on unencoded IDs for error form Compare: https://github.com/galaxyproject/galaxy/compare/ea785ea59837...8cc10c98ec45

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[galaxyproject/galaxy] 99f9d7: Use the datetime object instead of a string for pr...
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99f9d7724c53326330a41fa6a1b1c36624fef02d https://github.com/galaxyproject/galaxy/commit/99f9d7724c53326330a41fa6a1b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Use the datetime object instead of a string for pretty interval formatting. Commit: ea785ea598371f7aef0b37df59996e892d82f281 https://github.com/galaxyproject/galaxy/commit/ea785ea598371f7aef0b37df5999… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #1339 from dannon/library_datetime_tweak Use the datetime object instead of a string for pretty interval formatting. Compare: https://github.com/galaxyproject/galaxy/compare/0c8df84685c5...ea785ea59837

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