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

[galaxyproject/galaxy] 89c811: Move 'Copy History Items' to the bottom of the sec...
by GitHub 25 Aug '17

25 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89c811b790d7ef3508f361195ca4333903e5b955 https://github.com/galaxyproject/galaxy/commit/89c811b790d7ef3508f361195ca4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M templates/webapps/galaxy/dataset/copy_view.mako Log Message: ----------- Move 'Copy History Items' to the bottom of the second column in the old copy histories page. Commit: 426aa310fd21f320767b575dcd209ae63ad88b24 https://github.com/galaxyproject/galaxy/commit/426aa310fd21f320767b575dcd20… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M templates/webapps/galaxy/dataset/copy_view.mako Log Message: ----------- Merge pull request #4486 from dannon/copy_history_minor_improvement Minor copy datasets dialog improvement. Compare: https://github.com/galaxyproject/galaxy/compare/0010f6c0d8ab...426aa310fd21

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[galaxyproject/galaxy] f5ac8c: add mz5 datatype
by GitHub 25 Aug '17

25 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5ac8ce30d369c3661a8e1e4ea8424a540a41f66 https://github.com/galaxyproject/galaxy/commit/f5ac8ce30d369c3661a8e1e4ea84… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add mz5 datatype Commit: 0010f6c0d8ab7ad128ba4bfefd406dccc9bc5e9f https://github.com/galaxyproject/galaxy/commit/0010f6c0d8ab7ad128ba4bfefd40… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #4466 from bgruening/mz5 add mz5 datatype Compare: https://github.com/galaxyproject/galaxy/compare/df0507e49420...0010f6c0d8ab

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[galaxyproject/galaxy] 3ef39b: Fix drag and drop from history for firefox
by GitHub 25 Aug '17

25 Aug '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 3ef39b390c8d2f66ff890a29b712f785b6376601 https://github.com/galaxyproject/galaxy/commit/3ef39b390c8d2f66ff890a29b712… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Fix drag and drop from history for firefox Commit: cf897795fe8b544bc4cb5899585b1be2ee0063e6 https://github.com/galaxyproject/galaxy/commit/cf897795fe8b544bc4cb5899585b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge pull request #4496 from guerler/fix_drag_drop_firefox [17.05] Fix drag and drop from history for Firefox Compare: https://github.com/galaxyproject/galaxy/compare/685b9de09bca...cf897795fe8b

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[galaxyproject/galaxy] ae4877: needed for sentry functionality in reports webapp
by GitHub 25 Aug '17

25 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ae48774f54f317c2417b7677f1ef6cfde662a5f4 https://github.com/galaxyproject/galaxy/commit/ae48774f54f317c2417b7677f1ef… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/webapps/reports/config.py Log Message: ----------- needed for sentry functionality in reports webapp Commit: 0e467b73bcb1c6493bda6997bb133c19b72a275d https://github.com/galaxyproject/galaxy/commit/0e467b73bcb1c6493bda6997bb13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/webapps/reports/config.py Log Message: ----------- Fixes for reports sentry dsn (lint and missing import). Commit: f09b5c5b9de02d66fbca836bbe5a19a8f1e66dfb https://github.com/galaxyproject/galaxy/commit/f09b5c5b9de02d66fbca836bbe5a… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/galaxy/webapps/reports/config.py Log Message: ----------- Merge pull request #19 from dannon/reports-sentry-dsn Fixes for reports sentry dsn (lint and missing import). Commit: df0507e494208018ff19c71d17afb9f5c4b3b6ce https://github.com/galaxyproject/galaxy/commit/df0507e494208018ff19c71d17af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/galaxy/webapps/reports/config.py Log Message: ----------- Merge pull request #4471 from erasche/reports-sentry-dsn needed for sentry functionality in reports webapp Compare: https://github.com/galaxyproject/galaxy/compare/c89233c7cbbe...df0507e49420

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[galaxyproject/galaxy] da5b72: Alias `bcf_bgzip` datatype to `bcf`. Add `bcf_unco...
by GitHub 25 Aug '17

25 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: da5b72a030d8d07c663566527fc64560e067eb54 https://github.com/galaxyproject/galaxy/commit/da5b72a030d8d07c663566527fc6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed Log Message: ----------- Alias `bcf_bgzip` datatype to `bcf`. Add `bcf_uncompressed` and converters Since https://bitbucket.org/galaxy/galaxy-central/pull-requests/353 (only) compressed BCF files have been sniffed as `bcf`, so the `bcf_bgzip` datatype (introduced 2 years later in https://github.com/galaxyproject/galaxy/pull/1148 ) is an unused duplicate. This adds also a distinct `bcf_uncompressed` datatype (and converters) for the rare cases when it may be useful. Commit: 8dc0e697d3f8841270f6d934d19b271cf23b219e https://github.com/galaxyproject/galaxy/commit/8dc0e697d3f8841270f6d934d19b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix `vcf_bgzip` datatype In https://github.com/galaxyproject/galaxy/pull/4254 `vcf_bgzip` was made a proper datatype with the introduction of the `VcfGz` class, but was still described as a subclass in `datatypes_conf.xml` . Also fix `file_ext` attribute in `BaseVcf` and subclasses. Commit: a63af63b41e81a104dc177cb13dc2f6f3b4e9e6d https://github.com/galaxyproject/galaxy/commit/a63af63b41e81a104dc177cb13dc… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml Log Message: ----------- Add requirement for bcftools to set_metadata tool The `bcftools` binary is used by the `set_meta()` method of the `Bcf` datatype class. Having a `<requirement>` for it in the set_metadata tool makes it possible to use conda to resolve the dependency instead of forcing the admin to install `bcftools` on the PATH of the Galaxy user. This will also fix errors like https://travis-ci.org/galaxyproject/tools-iuc/jobs/266923024#L1994 when running ``` planemo test --conda_dependency_resolution --conda_auto_install ``` Commit: c89233c7cbbe263d3670fd5d4066a83f537ee173 https://github.com/galaxyproject/galaxy/commit/c89233c7cbbe263d3670fd5d4066… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.bcf A lib/galaxy/datatypes/test/1.bcf_uncompressed M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4477 from nsoranzo/vcf_bcf_fixes Fixes for VCF/BCF datatypes Compare: https://github.com/galaxyproject/galaxy/compare/1426225a78d0...c89233c7cbbe

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[galaxyproject/galaxy] b80ee7: Remove /mobile and associated templates. It has b...
by GitHub 24 Aug '17

24 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b80ee79b4302bd208ce5aa1fb86fb58e2b89a0c7 https://github.com/galaxyproject/galaxy/commit/b80ee79b4302bd208ce5aa1fb86f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: R lib/galaxy/webapps/galaxy/controllers/mobile.py R templates/webapps/galaxy/mobile/dataset/detail.mako R templates/webapps/galaxy/mobile/dataset/peek.mako R templates/webapps/galaxy/mobile/form.mako R templates/webapps/galaxy/mobile/history/detail.mako R templates/webapps/galaxy/mobile/history/list.mako R templates/webapps/galaxy/mobile/index.mako R templates/webapps/galaxy/mobile/manage_library.mako R templates/webapps/galaxy/mobile/settings.mako Log Message: ----------- Remove /mobile and associated templates. It has been deactivated for almost three years now. Commit: e542c47872881964c9c5fd0220904caee16f868a https://github.com/galaxyproject/galaxy/commit/e542c47872881964c9c5fd022090… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: R client/galaxy/style/less/iphone.less M client/grunt-tasks/style.js M static/scripts/bundled/admin.bundled.js.map 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/bundled/login.bundled.js.map R static/style/blue/iphone.css Log Message: ----------- Remove ancient 'iphone' styling that is unused (and missing assets) Commit: 4c14de6955a6c2fef489fd9603aec4e88df65539 https://github.com/galaxyproject/galaxy/commit/4c14de6955a6c2fef489fd9603ae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/jquery/jqtouch.js M client/grunt-tasks/install-libs.js R static/jqtouch/img/backButton.png R static/jqtouch/img/back_button.png R static/jqtouch/img/back_button_clicked.png R static/jqtouch/img/bg_row.gif R static/jqtouch/img/bg_row_select.gif R static/jqtouch/img/blueButton.png R static/jqtouch/img/button.png R static/jqtouch/img/button_clicked.png R static/jqtouch/img/cancel.png R static/jqtouch/img/chevron.png R static/jqtouch/img/chevron_select.png R static/jqtouch/img/grayButton.png R static/jqtouch/img/header.gif R static/jqtouch/img/listGroup.png R static/jqtouch/img/loading.gif R static/jqtouch/img/pinstripes.png R static/jqtouch/img/selection.png R static/jqtouch/img/thumb.png R static/jqtouch/img/toggle.png R static/jqtouch/img/toggleOn.png R static/jqtouch/img/toolButton.png R static/jqtouch/img/toolbar.gif R static/jqtouch/img/toolbar.png R static/jqtouch/img/whiteButton.png R static/jqtouch/jqtouch.css Log Message: ----------- strip jqtouch Commit: 1426225a78d0adc7a024d33f314bdfa613eabe5d https://github.com/galaxyproject/galaxy/commit/1426225a78d0adc7a024d33f314b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/jquery/jqtouch.js R client/galaxy/style/less/iphone.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js R lib/galaxy/webapps/galaxy/controllers/mobile.py R static/jqtouch/img/backButton.png R static/jqtouch/img/back_button.png R static/jqtouch/img/back_button_clicked.png R static/jqtouch/img/bg_row.gif R static/jqtouch/img/bg_row_select.gif R static/jqtouch/img/blueButton.png R static/jqtouch/img/button.png R static/jqtouch/img/button_clicked.png R static/jqtouch/img/cancel.png R static/jqtouch/img/chevron.png R static/jqtouch/img/chevron_select.png R static/jqtouch/img/grayButton.png R static/jqtouch/img/header.gif R static/jqtouch/img/listGroup.png R static/jqtouch/img/loading.gif R static/jqtouch/img/pinstripes.png R static/jqtouch/img/selection.png R static/jqtouch/img/thumb.png R static/jqtouch/img/toggle.png R static/jqtouch/img/toggleOn.png R static/jqtouch/img/toolButton.png R static/jqtouch/img/toolbar.gif R static/jqtouch/img/toolbar.png R static/jqtouch/img/whiteButton.png R static/jqtouch/jqtouch.css M static/scripts/bundled/admin.bundled.js.map 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/bundled/login.bundled.js.map R static/style/blue/iphone.css R templates/webapps/galaxy/mobile/dataset/detail.mako R templates/webapps/galaxy/mobile/dataset/peek.mako R templates/webapps/galaxy/mobile/form.mako R templates/webapps/galaxy/mobile/history/detail.mako R templates/webapps/galaxy/mobile/history/list.mako R templates/webapps/galaxy/mobile/index.mako R templates/webapps/galaxy/mobile/manage_library.mako R templates/webapps/galaxy/mobile/settings.mako Log Message: ----------- Merge pull request #4494 from dannon/no_mobile Remove /mobile and associated templates Compare: https://github.com/galaxyproject/galaxy/compare/5ae1446970ec...1426225a78d0

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[galaxyproject/galaxy] 5d04c5: Removes unused comma from subworkflow populator
by GitHub 24 Aug '17

24 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5d04c593b637146c69eed1b6909a74c67ab4de1a https://github.com/galaxyproject/galaxy/commit/5d04c593b637146c69eed1b6909a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Removes unused comma from subworkflow populator Commit: 5ae1446970ec43e578ab400f529bd753cd81d052 https://github.com/galaxyproject/galaxy/commit/5ae1446970ec43e578ab400f529b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4492 from guerler/fix_subworkflow_comma Remove unused comma from subworkflow populator Compare: https://github.com/galaxyproject/galaxy/compare/001d94ae4ea0...5ae1446970ec

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[galaxyproject/galaxy] d3ae73: Use pysam instead of samtools binary
by GitHub 24 Aug '17

24 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3ae7351f734b4e841c91495c1e41c77fe4e01b1 https://github.com/galaxyproject/galaxy/commit/d3ae7351f734b4e841c91495c1e4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Use pysam instead of samtools binary This will make it possible to remove the requirement of having `samtools` installed when testing tools, e.g. in the tools-iuc TravisCI setup: https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L59 Commit: 001d94ae4ea0af1ed16c809a6e8e26c356549396 https://github.com/galaxyproject/galaxy/commit/001d94ae4ea0af1ed16c809a6e8e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Merge pull request #4479 from nsoranzo/use_pysam_in_verify Use pysam instead of samtools binary Compare: https://github.com/galaxyproject/galaxy/compare/a83438159c2a...001d94ae4ea0

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[galaxyproject/galaxy] 30562c: don't uppercase envoverride
by GitHub 23 Aug '17

23 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30562c09c54e112f141a91635e91aa942ff4ece7 https://github.com/galaxyproject/galaxy/commit/30562c09c54e112f141a91635e91… Author: xgaia <xgaia(a)gmx.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- don't uppercase envoverride Commit: a83438159c2aa8d92b9c9f53ec64f9188ec94a8f https://github.com/galaxyproject/galaxy/commit/a83438159c2aa8d92b9c9f53ec64… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #4458 from xgaia/interactive_environment don't uppercase envoverride Compare: https://github.com/galaxyproject/galaxy/compare/27bd71332a66...a83438159c2a

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[galaxyproject/galaxy] a6632f: replace exclamation with a clock icon
by GitHub 23 Aug '17

23 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a6632f31338911176052db99257aa8f825286008 https://github.com/galaxyproject/galaxy/commit/a6632f31338911176052db99257a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M client/galaxy/style/less/dataset.less M static/scripts/bundled/admin.bundled.js.map 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/bundled/login.bundled.js.map M static/style/blue/base.css Log Message: ----------- replace exclamation with a clock icon Commit: 27bd71332a66195f66536825d6da05ed505330f1 https://github.com/galaxyproject/galaxy/commit/27bd71332a66195f66536825d6da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M client/galaxy/style/less/dataset.less M static/scripts/bundled/admin.bundled.js.map 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/bundled/login.bundled.js.map M static/style/blue/base.css Log Message: ----------- Merge pull request #4485 from martenson/remove-exclamation replace exclamation with a clock icon Compare: https://github.com/galaxyproject/galaxy/compare/63d1d428a1d9...27bd71332a66

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