- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 053f51: forgoten minification and map
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 053f51eb537a4624bc0751c0ae39efb59eb996ea https://github.com/galaxyproject/galaxy/commit/053f51eb537a4624bc0751c0ae39… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-view.js Log Message: ----------- forgoten minification and map Commit: 3201005739ab5071399a55b0aa99682ffb539c26 https://github.com/galaxyproject/galaxy/commit/3201005739ab5071399a55b0aa99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-view.js Log Message: ----------- Merge pull request #850 from martenson/forgotten-minification forgoten minification and map Compare: https://github.com/galaxyproject/galaxy/compare/4cd4dac0a088...3201005739ab

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[galaxyproject/galaxy] f50702: Remove unused echo tool
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f50702f96253d1d4a6ad1dbe088b1d04c6e1506a https://github.com/galaxyproject/galaxy/commit/f50702f96253d1d4a6ad1dbe088b… Author: Eric Rasche <rasche.eric(a)yandex.ru> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R tools/data_source/echo.py R tools/data_source/echo.xml Log Message: ----------- Remove unused echo tool Commit: 4cd4dac0a088b3d040766853fee8b179d94f144a https://github.com/galaxyproject/galaxy/commit/4cd4dac0a088b3d040766853fee8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R tools/data_source/echo.py R tools/data_source/echo.xml Log Message: ----------- Merge pull request #848 from jmchilton/echo_remove Remove unused echo tool Compare: https://github.com/galaxyproject/galaxy/compare/753bb9de0fa0...4cd4dac0a088

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[galaxyproject/galaxy] 4e35ff: More improved file handling for job code.
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e35ff04a116a4a9ca1d96e9b3c5842be9fa9f7f https://github.com/galaxyproject/galaxy/commit/4e35ff04a116a4a9ca1d96e9b3c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- More improved file handling for job code. Another stab in the dark that won't actually fix the testing issues with Docker. Commit: b75175f18d15000a2dc5826f49424eba6dc7d489 https://github.com/galaxyproject/galaxy/commit/b75175f18d15000a2dc5826f4942… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Centralize logic for writing job scripts. Runners were using various permissions, some didn't close file handles, etc.... In addition, run sync after script is written to avoid "Text file busy" problems in all job script scenerios. Commit: 753bb9de0fa031720b8c7881ff1d52cbf6a522d3 https://github.com/galaxyproject/galaxy/commit/753bb9de0fa031720b8c7881ff1d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Merge pull request #839 from jmchilton/text_file_busy Attempt to fix "Text file busy" errors (testing and production) Compare: https://github.com/galaxyproject/galaxy/compare/bb43ace50927...753bb9de0fa0

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[galaxyproject/galaxy] 6430b9: Update documentation for the gff_filter_by_attribu...
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6430b9c4e834161910c23438f9fd779b78846de7 https://github.com/galaxyproject/galaxy/commit/6430b9c4e834161910c23438f9fd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/filters/gff/gff_filter_by_attribute.xml Log Message: ----------- Update documentation for the gff_filter_by_attribute tool Commit: bb43ace5092799e49875589f6da7404806e27137 https://github.com/galaxyproject/galaxy/commit/bb43ace5092799e49875589f6da7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M tools/filters/gff/gff_filter_by_attribute.xml Log Message: ----------- Merge pull request #842 from bgruening/filter_by_attribute Update documentation for the gff_filter_by_attribute tool Compare: https://github.com/galaxyproject/galaxy/compare/3687d45a0371...bb43ace50927

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[galaxyproject/galaxy] 54410d: Use eggs.require() instead of pkg_resources in lib...
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54410d7d70c13c76ac370e83c12db7810192fc71 https://github.com/galaxyproject/galaxy/commit/54410d7d70c13c76ac370e83c12d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Use eggs.require() instead of pkg_resources in lib/galaxy/datatypes/ . Fix https://github.com/galaxyproject/galaxy/issues/809#issuecomment-145107037 . Commit: 3687d45a037166e2fffcdfe7fda4cfd6d2b08346 https://github.com/galaxyproject/galaxy/commit/3687d45a037166e2fffcdfe7fda4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #838 from nsoranzo/pkg_resources Use eggs.require() instead of pkg_resources in lib/galaxy/datatypes/ . Compare: https://github.com/galaxyproject/galaxy/compare/0a83a244f170...3687d45a0371

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[galaxyproject/galaxy] 2210f8: Remove run_functional_tests.sh.
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2210f83da95b702ea10f7809b29ee77d54fc1529 https://github.com/galaxyproject/galaxy/commit/2210f83da95b702ea10f7809b29e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R run_functional_tests.sh Log Message: ----------- Remove run_functional_tests.sh. It has been deprecated who a while and removed once already - hopefully now we can kill it. Commit: 596f9116f25f384899f9c7acb5517d57b88ca358 https://github.com/galaxyproject/galaxy/commit/596f9116f25f384899f9c7acb551… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Use framework test tools for --api and --casperjs tests. These tests are explicitly designed to test the framework and use a tool panel. ``sh run_tests.sh`` and ``sh run_tests.sh -id`` are meant to test Galaxy's configuration to some degree, and other tests qunit, unit, and toolshed do not depend on the toolbox. Commit: 0a83a244f170226ec02f41a9972bd9bfcb261449 https://github.com/galaxyproject/galaxy/commit/0a83a244f170226ec02f41a9972b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R run_functional_tests.sh M run_tests.sh Log Message: ----------- Merge pull request #844 from jmchilton/run_test_adjustments More small adjustments to test script. Compare: https://github.com/galaxyproject/galaxy/compare/7dcd2636fd83...0a83a244f170

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[galaxyproject/galaxy] f64a23: initial implementation of library search
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f64a23fbe16d2af956840ffef673f6455700249f https://github.com/galaxyproject/galaxy/commit/f64a23fbe16d2af956840ffef673… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- initial implementation of library search Commit: 91ef04a25bdc5962ce650d925db5f8a94c345d06 https://github.com/galaxyproject/galaxy/commit/91ef04a25bdc5962ce650d925db5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- docs, refac and indentation Commit: 7dcd2636fd83dc935306cbd405091c60c1d54bdf https://github.com/galaxyproject/galaxy/commit/7dcd2636fd83dc935306cbd40509… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- Merge pull request #820 from martenson/lib-search Initial implementation of data library search Compare: https://github.com/galaxyproject/galaxy/compare/51a3f5414064...7dcd2636fd83

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[galaxyproject/galaxy] e3364d: Update comment in sample.
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e3364d6db428d0695ce978dfa0604e775da11f67 https://github.com/galaxyproject/galaxy/commit/e3364d6db428d0695ce978dfa060… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Update comment in sample. Commit: 51a3f5414064d0b927023cb9e0096995e0470b8d https://github.com/galaxyproject/galaxy/commit/51a3f5414064d0b927023cb9e009… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #841 from dannon/default_debug_off Update comment in sample. Compare: https://github.com/galaxyproject/galaxy/compare/a92ed830ee66...51a3f5414064

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[galaxyproject/galaxy] 1564dc: Swap debug mode to be off by default in galaxy.ini...
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1564dc665be8e2a44cb3298f22e0d70811205c15 https://github.com/galaxyproject/galaxy/commit/1564dc665be8e2a44cb3298f22e0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Swap debug mode to be off by default in galaxy.ini.sample. Commit: a92ed830ee66719708b062b39f64092741a83975 https://github.com/galaxyproject/galaxy/commit/a92ed830ee66719708b062b39f64… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #840 from dannon/default_debug_off Swap debug mode to be off by default in galaxy.ini.sample. Compare: https://github.com/galaxyproject/galaxy/compare/a47f9defe322...a92ed830ee66

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[galaxyproject/galaxy] 4e3fe5: Fix to a5e97e6: correctly pass in dom fragment to ...
by GitHub 02 Oct '15

02 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e3fe5012f295e9f64c81b914332068a8a04d8fb https://github.com/galaxyproject/galaxy/commit/4e3fe5012f295e9f64c81b914332… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel-edit-current.js M static/maps/mvc/history/history-panel-edit-current.js.map M static/scripts/mvc/history/history-panel-edit-current.js Log Message: ----------- Fix to a5e97e6: correctly pass in dom fragment to setUpBehaviors (fixes multiselect btn and name editing Commit: a47f9defe32211b8b589794a7a761889b053326c https://github.com/galaxyproject/galaxy/commit/a47f9defe32211b8b589794a7a76… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel-edit-current.js M static/maps/mvc/history/history-panel-edit-current.js.map M static/scripts/mvc/history/history-panel-edit-current.js Log Message: ----------- Merge pull request #834 from carlfeberhard/fix.multiselect Fix to a5e97e6: correctly pass in dom fragment to setUpBehaviors (fix… Compare: https://github.com/galaxyproject/galaxy/compare/02962ae64680...a47f9defe322

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