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[galaxyproject/galaxy] aaf09d: Generate metadata in separate conda environment
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aaf09dc99b0dc2896cbba5d21c132e998f5126e7 https://github.com/galaxyproject/galaxy/commit/aaf09dc99b0dc2896cbba5d21c13… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Generate metadata in separate conda environment Galaxy supports generating metadata in a separate command (enable beta_tool_command_isolation). This command has its own dependency resolution, that may interfere with thedependency resolution of the actual tool, if the same environment is being used. With this PR we create a new environment when resolving metadata dependencies with conda, that will be active only for metadata generation. Commit: 5dd9d1bafcc4532fdb48b312a47e2f90b7178d80 https://github.com/galaxyproject/galaxy/commit/5dd9d1bafcc4532fdb48b312a47e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix whitespace and comma use Commit: a7bcd69f9e6b72279772cc9ca003408df830e881 https://github.com/galaxyproject/galaxy/commit/a7bcd69f9e6b72279772cc9ca003… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2253 from mvdbeek/conda-metadata-env Generate metadata in separate conda environment Compare: https://github.com/galaxyproject/galaxy/compare/8a3b5d3d3e36...a7bcd69f9e6b

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[galaxyproject/galaxy] 4630c6: Tool execution dependency resolution already conta...
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4630c6417d4e2c0ec747df02d28578f9576bb2a4 https://github.com/galaxyproject/galaxy/commit/4630c6417d4e2c0ec747df02d285… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Tool execution dependency resolution already contains the relevant information for viewing dependency resolution attempts and warns when the dependency isn't found (Null resolver). Pretty sure this was just a stray extra debugging statement that got unintentionally left in, and it's pretty chatty. Commit: 8a3b5d3d3e36946f240b55de071b75e4c0fa2e07 https://github.com/galaxyproject/galaxy/commit/8a3b5d3d3e36946f240b55de071b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #2254 from dannon/remove_dep_debugging Tool execution dependency resolution already contains the relevant Compare: https://github.com/galaxyproject/galaxy/compare/e2287e2c9dd6...8a3b5d3d3e36

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[galaxyproject/galaxy] bf5568: Quote some parameters in Trim tool command
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf5568d86ae2e111ab90b9658192ee70faf11fc7 https://github.com/galaxyproject/galaxy/commit/bf5568d86ae2e111ab90b9658192… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M tools/filters/trimmer.xml Log Message: ----------- Quote some parameters in Trim tool command Make the tool more robust, see issue #2245. Also: - use format_source instead of deprecated format='input'; - explicitly call python in command instead of using the depredated interpreter attribute; - use CDATA in command. Commit: e2287e2c9dd6cf394dbb30b1e77123a25a29d8f5 https://github.com/galaxyproject/galaxy/commit/e2287e2c9dd6cf394dbb30b1e771… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M tools/filters/trimmer.xml Log Message: ----------- Merge pull request #2248 from nsoranzo/fix_trimmer_tool Quote some parameters in Trim tool command Compare: https://github.com/galaxyproject/galaxy/compare/d7031d982219...e2287e2c9dd6

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[galaxyproject/galaxy] 7718ac: Rename Utils.validate() to Utils.isEmpty()
by GitHub 27 Apr '16

27 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7718ac511b87078c48a2c6d1f396990e6dbb7f1a https://github.com/galaxyproject/galaxy/commit/7718ac511b87078c48a2c6d1f396… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js Log Message: ----------- Rename Utils.validate() to Utils.isEmpty() Commit: faa2e69ec72e51b10e8a8d96a3a92b2868192c6e https://github.com/galaxyproject/galaxy/commit/faa2e69ec72e51b10e8a8d96a3a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: A test/qunit/tests/utils_test.html A test/qunit/tests/utils_test.js Log Message: ----------- Add test cases Commit: d7031d982219c1530a83d645cf897dc609fb6431 https://github.com/galaxyproject/galaxy/commit/d7031d982219c1530a83d645cf89… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js A test/qunit/tests/utils_test.html A test/qunit/tests/utils_test.js Log Message: ----------- Merge pull request #2239 from guerler/rename_jsvalidate_000 Rename/refactor Utils.validate() to Utils.isEmpty() Compare: https://github.com/galaxyproject/galaxy/compare/01472fdc0188...d7031d982219

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[galaxyproject/usegalaxy-playbook] f019c1: Update main version
by GitHub 26 Apr '16

26 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f019c1a2e581a5ae5e2f75fe26ea265d9f8c4514 https://github.com/galaxyproject/usegalaxy-playbook/commit/f019c1a2e581a5ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-26 (Tue, 26 Apr 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update main version

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[galaxyproject/galaxy] e87569: add TS API to check current user
by GitHub 25 Apr '16

25 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8756907039de8fa9f3a2c571c987982d716bc54 https://github.com/galaxyproject/galaxy/commit/e8756907039de8fa9f3a2c571c98… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/users.py Log Message: ----------- add TS API to check current user Commit: 01472fdc018823527968d6e78fb2255cdfbed271 https://github.com/galaxyproject/galaxy/commit/01472fdc018823527968d6e78fb2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/users.py Log Message: ----------- Merge pull request #2243 from martenson/check-curr-ts-user add TS API to check current user Compare: https://github.com/galaxyproject/galaxy/compare/af4ebccebbc6...01472fdc0188

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[galaxyproject/galaxy] 5749e3: Encode collection reduce in serializable fashion
by GitHub 25 Apr '16

25 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5749e3484bffdc0b066f281d0708ffe3228d5415 https://github.com/galaxyproject/galaxy/commit/5749e3484bffdc0b066f281d0708… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Encode collection reduce in serializable fashion Commit: ce31431f2949344d72c949d0ba5b495b0c90a1be https://github.com/galaxyproject/galaxy/commit/ce31431f2949344d72c949d0ba5b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-23 (Sat, 23 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #2238 from guerler/fix_collection_reduce_000 [16.04] Encode collection reduce in serializable fashion Commit: af4ebccebbc66551e1ab71400fa6e7ac4b6dae33 https://github.com/galaxyproject/galaxy/commit/af4ebccebbc66551e1ab71400fa6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-25 (Mon, 25 Apr 2016) Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2c56b5f995e3...af4ebccebbc6

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[galaxyproject/galaxy] 18556b: Encode collection reduce in serializable fashion
by GitHub 25 Apr '16

25 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18556be6fcbd53bcec88e233e8cd856309e404ae https://github.com/galaxyproject/galaxy/commit/18556be6fcbd53bcec88e233e8cd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-24 (Sun, 24 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Encode collection reduce in serializable fashion Commit: 2c56b5f995e356de0bb446577ac96ff4f1ee0f4c https://github.com/galaxyproject/galaxy/commit/2c56b5f995e356de0bb446577ac9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #2241 from guerler/fix_test_000 Encode collection reduce in serializable fashion Compare: https://github.com/galaxyproject/galaxy/compare/18a6393010d1...2c56b5f995e3

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[galaxyproject/galaxy] c2b091: Tests demonstrating multi-data params in repeats a...
by GitHub 23 Apr '16

23 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2b091d207197759e9693b6d5bf3581a678043ee https://github.com/galaxyproject/galaxy/commit/c2b091d207197759e9693b6d5bf3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M test/api/test_tools.py A test/functional/tools/multi_data_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Tests demonstrating multi-data params in repeats are broken. A test cases and a tool that can be tested directory. Commit: 18a6393010d17d0477ecafeb98c29595f0b9ec34 https://github.com/galaxyproject/galaxy/commit/18a6393010d17d0477ecafeb98c2… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-23 (Sat, 23 Apr 2016) Changed paths: M test/api/test_tools.py A test/functional/tools/multi_data_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2233 from jmchilton/repeat_multidata [16.04] Multi-data collection reductions in repeat blocks are broken. Compare: https://github.com/galaxyproject/galaxy/compare/581e5ccdcb21...18a6393010d1

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[galaxyproject/galaxy] 5749e3: Encode collection reduce in serializable fashion
by GitHub 23 Apr '16

23 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 5749e3484bffdc0b066f281d0708ffe3228d5415 https://github.com/galaxyproject/galaxy/commit/5749e3484bffdc0b066f281d0708… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Encode collection reduce in serializable fashion Commit: ce31431f2949344d72c949d0ba5b495b0c90a1be https://github.com/galaxyproject/galaxy/commit/ce31431f2949344d72c949d0ba5b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-23 (Sat, 23 Apr 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #2238 from guerler/fix_collection_reduce_000 [16.04] Encode collection reduce in serializable fashion Compare: https://github.com/galaxyproject/galaxy/compare/62bc415ae6ed...ce31431f2949

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