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

[galaxyproject/galaxy] 2625bc: Fix flake8 broken when merging 041c94bf788bea09904...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2625bc4bc02f3b109c2340ca46b376fc9fbd9017 https://github.com/galaxyproject/galaxy/commit/2625bc4bc02f3b109c2340ca46b3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Fix flake8 broken when merging 041c94bf788bea0990401dab14e0ab717cec0c55 from release_15.07 . Commit: 88c57bf16b52c8d7edbe0c91eb30dda277d4f24b https://github.com/galaxyproject/galaxy/commit/88c57bf16b52c8d7edbe0c91eb30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #688 from nsoranzo/dev Fix flake8 broken when merging from release_15.07 . Compare: https://github.com/galaxyproject/galaxy/compare/bcbeb75a6895...88c57bf16b52

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[galaxyproject/galaxy] 8cd94b: When uploading tool_dependencies.xml to toolshed, ...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8cd94be52d5030634e843a89d7025ecb6f18394b https://github.com/galaxyproject/galaxy/commit/8cd94be52d5030634e843a89d702… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- When uploading tool_dependencies.xml to toolshed, do set toolshed repository attributes of package/repository tags that occur within actions that specify os or architecture. Commit: b01d20b1be9e1cf579a3c2bd42a3d524548d2240 https://github.com/galaxyproject/galaxy/commit/b01d20b1be9e1cf579a3c2bd42a3… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Fix for server error when installing some repos. Examples: IUC's gatk2 repository, devteam's samtools_rmdup. When attempting to install either of those, or another repository that has tool tests with an input parameter that does not have a value attribute, the repository would be stuck in state 'Cloning' and show a debug link in the log. This commit resolves that error. Commit: 19c85e070534f4318cca3e728c52c91a27163f4a https://github.com/galaxyproject/galaxy/commit/19c85e070534f4318cca3e728c52… Author: Jeremy Goecks <jgoecks(a)gwu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/viz/sweepster.js M static/maps/mvc/tools.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/viz/sweepster.js Log Message: ----------- Fixes to make Sweepster work again: (a) update template syntax to match changes made in underscore v1.7 and (b) update tool rerun to account for API changes. Commit: 04a5bd78f021968ccd1b98eec2968ecdc3c93f77 https://github.com/galaxyproject/galaxy/commit/04a5bd78f021968ccd1b98eec296… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix: rdata extension type Commit: a1cc1ed94bba19bcc131f41d6cfc80fe1ca03009 https://github.com/galaxyproject/galaxy/commit/a1cc1ed94bba19bcc131f41d6cfc… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix: Typo the other way. Supposed to be "RData" Ref: https://stat.ethz.ch/R-manual/R-devel/library/base/html/save.html Commit: ac43237e49e8660b1812f8662d081d4b0d3bf3de https://github.com/galaxyproject/galaxy/commit/ac43237e49e8660b1812f8662d08… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- Fix for toolshed escape method, where an error/log message contains non-ASCII characters. Commit: d2e61e8af4c933b733c640f46f831bf424bc0197 https://github.com/galaxyproject/galaxy/commit/d2e61e8af4c933b733c640f46f83… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Filter deleted library datasets Commit: 8d96580fc20e2a6322fdacb1b25635fb4573c934 https://github.com/galaxyproject/galaxy/commit/8d96580fc20e2a6322fdacb1b256… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Correct examples in workflow invocations. Commit: 51991f03caf3b1ed15d4672160cf0f50e6e537db https://github.com/galaxyproject/galaxy/commit/51991f03caf3b1ed15d4672160cf… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: R templates/webapps/tool_shed/message.mako Log Message: ----------- Stop creating database/message.mako.py Commit: 64edf4e2f953f21e4e52c6647a65960c6c44945a https://github.com/galaxyproject/galaxy/commit/64edf4e2f953f21e4e52c6647a65… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M templates/webapps/reports/base_panels.mako Log Message: ----------- fix the class for reports brand so it is actually shown and not black text on dark background Commit: 041c94bf788bea0990401dab14e0ab717cec0c55 https://github.com/galaxyproject/galaxy/commit/041c94bf788bea0990401dab14e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M scripts/bootstrap_history.py Log Message: ----------- Release notes for 15.07. This includes a script to boot strap the notes for future releases, updated announcement page for 15.07, and new announcement page for 15.10. Commit: 4a05c07aa5cc8e386742bb638a6c44e839efc9bd https://github.com/galaxyproject/galaxy/commit/4a05c07aa5cc8e386742bb638a6c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A scripts/bootstrap_history_announce_template.rst Log Message: ----------- Fixup end of release items for release notes. Commit: 65f39b2eaf6b0c94b1044a92351c2b5799ca021a https://github.com/galaxyproject/galaxy/commit/65f39b2eaf6b0c94b1044a92351c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Typo noticed by @martenson. Commit: 4fcdf9fda1d21ec5669daa8e9a4e3e84171bb617 https://github.com/galaxyproject/galaxy/commit/4fcdf9fda1d21ec5669daa8e9a4e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/viz/sweepster.js M lib/galaxy/datatypes/binary.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/web_util.py M static/maps/mvc/tools.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/viz/sweepster.js M templates/webapps/reports/base_panels.mako R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge pull request #657 from jmchilton/dev_1507_backports [15.07] Backport various dev fixes. Commit: a460ebd7d6b6132fe00238e834dcff0efb449ad8 https://github.com/galaxyproject/galaxy/commit/a460ebd7d6b6132fe00238e834dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst Log Message: ----------- Fix for explicit markup ending without a blank line Commit: 51534edc63bb7758d4fb4a7aaec13df7a1e5e8eb https://github.com/galaxyproject/galaxy/commit/51534edc63bb7758d4fb4a7aaec1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Deprecation notice for cloudlaunch Commit: 96840a3c57354690b9287e49dd2ef3400932b52e https://github.com/galaxyproject/galaxy/commit/96840a3c57354690b9287e49dd2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #9 from dannon/rn Deprecation notice for cloudlaunch. Commit: 82794e7ee7a8a6793438bf2021079515445bb873 https://github.com/galaxyproject/galaxy/commit/82794e7ee7a8a6793438bf202107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Fix cloudlaunch link. Commit: 36d262d7c695ba06c32f5c495a0a3ceb62d57731 https://github.com/galaxyproject/galaxy/commit/36d262d7c695ba06c32f5c495a0a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #10 from dannon/rn Fix cloudlaunch link. Commit: 525188d2a871fbb9b5e7438b18bb5412f62db975 https://github.com/galaxyproject/galaxy/commit/525188d2a871fbb9b5e7438b18bb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- Merge pull request #637 from blankenberg/recurse-toolshed-changeset-upload [release_15.07] Fix setting of toolshed repository attributes in special cases. Commit: 4dd6304f055706e38176823a4166c6536618a042 https://github.com/galaxyproject/galaxy/commit/4dd6304f055706e38176823a4166… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Fix version parsing in tool form Commit: 3653bf5e37b13ea17cecd321fdbe9ce4fedcfbb8 https://github.com/galaxyproject/galaxy/commit/3653bf5e37b13ea17cecd321fdbe… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge pull request #677 from guerler/fix_version_002 [15.07] Fix version handling in tool form Commit: f4605937e3bb1e0e993c66ac86deabff374034c4 https://github.com/galaxyproject/galaxy/commit/f4605937e3bb1e0e993c66ac86de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst Log Message: ----------- Merge pull request #642 from jmchilton/rn [15.07] Release notes for 15.07. Commit: f6b5558c11698069c4eebb1b28f089a3ecc32c40 https://github.com/galaxyproject/galaxy/commit/f6b5558c11698069c4eebb1b28f0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- For CSV type data, do not fail to set metadata when header and data row column counts mismatch. Commit: 099d61ef21e9cf1eae364cf807aa7e3705d8d787 https://github.com/galaxyproject/galaxy/commit/099d61ef21e9cf1eae364cf807aa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix for raising error when trying to compare unknown column types in CSV. Commit: 566acab16e52d3e9a1969366a2a52e02bf8c1eb9 https://github.com/galaxyproject/galaxy/commit/566acab16e52d3e9a1969366a2a5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #680 from blankenberg/csv_fix [15.07] For CSV type data, do not fail to set metadata when header and data row column counts mismatch. Commit: c2c1c723569db7076772235594f59e0dfe3a8c41 https://github.com/galaxyproject/galaxy/commit/c2c1c723569db7076772235594f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-installed tools, but the unfiltered info_dict was passed on, causing misalignment of repository and tsr_id. Commit: 990501d2d94741a3ac16016b8a37e48e84acf018 https://github.com/galaxyproject/galaxy/commit/990501d2d94741a3ac16016b8a37… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #687 from dannon/release_15.07 Backport of Fix issue #525 Commit: 4557b27fea515934fa5a9296c5993423aa482dd7 https://github.com/galaxyproject/galaxy/commit/4557b27fea515934fa5a9296c599… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/viz/sweepster.js A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/web_util.py M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/viz/sweepster.js M templates/webapps/reports/base_panels.mako R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge branch 'release_15.07' Commit: bcbeb75a68952597e89563d316dc0ec2d945f49c https://github.com/galaxyproject/galaxy/commit/bcbeb75a68952597e89563d316dc… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/tabular.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge branch 'master' into dev Conflicts: lib/tool_shed/dependencies/tool/tag_attribute_handler.py Compare: https://github.com/galaxyproject/galaxy/compare/f48dd9942567...bcbeb75a6895

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[galaxyproject/galaxy] 8cd94b: When uploading tool_dependencies.xml to toolshed, ...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 8cd94be52d5030634e843a89d7025ecb6f18394b https://github.com/galaxyproject/galaxy/commit/8cd94be52d5030634e843a89d702… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-24 (Mon, 24 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- When uploading tool_dependencies.xml to toolshed, do set toolshed repository attributes of package/repository tags that occur within actions that specify os or architecture. Commit: b01d20b1be9e1cf579a3c2bd42a3d524548d2240 https://github.com/galaxyproject/galaxy/commit/b01d20b1be9e1cf579a3c2bd42a3… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Fix for server error when installing some repos. Examples: IUC's gatk2 repository, devteam's samtools_rmdup. When attempting to install either of those, or another repository that has tool tests with an input parameter that does not have a value attribute, the repository would be stuck in state 'Cloning' and show a debug link in the log. This commit resolves that error. Commit: 19c85e070534f4318cca3e728c52c91a27163f4a https://github.com/galaxyproject/galaxy/commit/19c85e070534f4318cca3e728c52… Author: Jeremy Goecks <jgoecks(a)gwu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/viz/sweepster.js M static/maps/mvc/tools.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/viz/sweepster.js Log Message: ----------- Fixes to make Sweepster work again: (a) update template syntax to match changes made in underscore v1.7 and (b) update tool rerun to account for API changes. Commit: 04a5bd78f021968ccd1b98eec2968ecdc3c93f77 https://github.com/galaxyproject/galaxy/commit/04a5bd78f021968ccd1b98eec296… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix: rdata extension type Commit: a1cc1ed94bba19bcc131f41d6cfc80fe1ca03009 https://github.com/galaxyproject/galaxy/commit/a1cc1ed94bba19bcc131f41d6cfc… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix: Typo the other way. Supposed to be "RData" Ref: https://stat.ethz.ch/R-manual/R-devel/library/base/html/save.html Commit: ac43237e49e8660b1812f8662d081d4b0d3bf3de https://github.com/galaxyproject/galaxy/commit/ac43237e49e8660b1812f8662d08… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- Fix for toolshed escape method, where an error/log message contains non-ASCII characters. Commit: d2e61e8af4c933b733c640f46f831bf424bc0197 https://github.com/galaxyproject/galaxy/commit/d2e61e8af4c933b733c640f46f83… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Filter deleted library datasets Commit: 8d96580fc20e2a6322fdacb1b25635fb4573c934 https://github.com/galaxyproject/galaxy/commit/8d96580fc20e2a6322fdacb1b256… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Correct examples in workflow invocations. Commit: 51991f03caf3b1ed15d4672160cf0f50e6e537db https://github.com/galaxyproject/galaxy/commit/51991f03caf3b1ed15d4672160cf… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: R templates/webapps/tool_shed/message.mako Log Message: ----------- Stop creating database/message.mako.py Commit: 64edf4e2f953f21e4e52c6647a65960c6c44945a https://github.com/galaxyproject/galaxy/commit/64edf4e2f953f21e4e52c6647a65… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M templates/webapps/reports/base_panels.mako Log Message: ----------- fix the class for reports brand so it is actually shown and not black text on dark background Commit: 041c94bf788bea0990401dab14e0ab717cec0c55 https://github.com/galaxyproject/galaxy/commit/041c94bf788bea0990401dab14e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M scripts/bootstrap_history.py Log Message: ----------- Release notes for 15.07. This includes a script to boot strap the notes for future releases, updated announcement page for 15.07, and new announcement page for 15.10. Commit: 4a05c07aa5cc8e386742bb638a6c44e839efc9bd https://github.com/galaxyproject/galaxy/commit/4a05c07aa5cc8e386742bb638a6c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A scripts/bootstrap_history_announce_template.rst Log Message: ----------- Fixup end of release items for release notes. Commit: 65f39b2eaf6b0c94b1044a92351c2b5799ca021a https://github.com/galaxyproject/galaxy/commit/65f39b2eaf6b0c94b1044a92351c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Typo noticed by @martenson. Commit: 4fcdf9fda1d21ec5669daa8e9a4e3e84171bb617 https://github.com/galaxyproject/galaxy/commit/4fcdf9fda1d21ec5669daa8e9a4e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/viz/sweepster.js M lib/galaxy/datatypes/binary.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/web_util.py M static/maps/mvc/tools.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/viz/sweepster.js M templates/webapps/reports/base_panels.mako R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge pull request #657 from jmchilton/dev_1507_backports [15.07] Backport various dev fixes. Commit: a460ebd7d6b6132fe00238e834dcff0efb449ad8 https://github.com/galaxyproject/galaxy/commit/a460ebd7d6b6132fe00238e834dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst Log Message: ----------- Fix for explicit markup ending without a blank line Commit: 51534edc63bb7758d4fb4a7aaec13df7a1e5e8eb https://github.com/galaxyproject/galaxy/commit/51534edc63bb7758d4fb4a7aaec1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Deprecation notice for cloudlaunch Commit: 96840a3c57354690b9287e49dd2ef3400932b52e https://github.com/galaxyproject/galaxy/commit/96840a3c57354690b9287e49dd2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #9 from dannon/rn Deprecation notice for cloudlaunch. Commit: 82794e7ee7a8a6793438bf2021079515445bb873 https://github.com/galaxyproject/galaxy/commit/82794e7ee7a8a6793438bf202107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Fix cloudlaunch link. Commit: 36d262d7c695ba06c32f5c495a0a3ceb62d57731 https://github.com/galaxyproject/galaxy/commit/36d262d7c695ba06c32f5c495a0a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M doc/source/releases/15.07_announce.rst Log Message: ----------- Merge pull request #10 from dannon/rn Fix cloudlaunch link. Commit: 525188d2a871fbb9b5e7438b18bb5412f62db975 https://github.com/galaxyproject/galaxy/commit/525188d2a871fbb9b5e7438b18bb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-28 (Fri, 28 Aug 2015) Changed paths: M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py Log Message: ----------- Merge pull request #637 from blankenberg/recurse-toolshed-changeset-upload [release_15.07] Fix setting of toolshed repository attributes in special cases. Commit: 4dd6304f055706e38176823a4166c6536618a042 https://github.com/galaxyproject/galaxy/commit/4dd6304f055706e38176823a4166… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Fix version parsing in tool form Commit: 3653bf5e37b13ea17cecd321fdbe9ce4fedcfbb8 https://github.com/galaxyproject/galaxy/commit/3653bf5e37b13ea17cecd321fdbe… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge pull request #677 from guerler/fix_version_002 [15.07] Fix version handling in tool form Commit: f4605937e3bb1e0e993c66ac86deabff374034c4 https://github.com/galaxyproject/galaxy/commit/f4605937e3bb1e0e993c66ac86de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst Log Message: ----------- Merge pull request #642 from jmchilton/rn [15.07] Release notes for 15.07. Commit: f6b5558c11698069c4eebb1b28f089a3ecc32c40 https://github.com/galaxyproject/galaxy/commit/f6b5558c11698069c4eebb1b28f0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- For CSV type data, do not fail to set metadata when header and data row column counts mismatch. Commit: 099d61ef21e9cf1eae364cf807aa7e3705d8d787 https://github.com/galaxyproject/galaxy/commit/099d61ef21e9cf1eae364cf807aa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix for raising error when trying to compare unknown column types in CSV. Commit: 566acab16e52d3e9a1969366a2a52e02bf8c1eb9 https://github.com/galaxyproject/galaxy/commit/566acab16e52d3e9a1969366a2a5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #680 from blankenberg/csv_fix [15.07] For CSV type data, do not fail to set metadata when header and data row column counts mismatch. Commit: c2c1c723569db7076772235594f59e0dfe3a8c41 https://github.com/galaxyproject/galaxy/commit/c2c1c723569db7076772235594f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-installed tools, but the unfiltered info_dict was passed on, causing misalignment of repository and tsr_id. Commit: 990501d2d94741a3ac16016b8a37e48e84acf018 https://github.com/galaxyproject/galaxy/commit/990501d2d94741a3ac16016b8a37… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #687 from dannon/release_15.07 Backport of Fix issue #525 Commit: 4557b27fea515934fa5a9296c5993423aa482dd7 https://github.com/galaxyproject/galaxy/commit/4557b27fea515934fa5a9296c599… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/viz/sweepster.js A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/web_util.py M scripts/bootstrap_history.py A scripts/bootstrap_history_announce_template.rst M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/viz/sweepster.js M templates/webapps/reports/base_panels.mako R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/224c20d4b2cf...4557b27fea51

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[galaxyproject/galaxy] c2c1c7: Fix issue #525. Repo info dicts and tsr_ids were f...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: c2c1c723569db7076772235594f59e0dfe3a8c41 https://github.com/galaxyproject/galaxy/commit/c2c1c723569db7076772235594f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-installed tools, but the unfiltered info_dict was passed on, causing misalignment of repository and tsr_id. Commit: 990501d2d94741a3ac16016b8a37e48e84acf018 https://github.com/galaxyproject/galaxy/commit/990501d2d94741a3ac16016b8a37… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #687 from dannon/release_15.07 Backport of Fix issue #525 Compare: https://github.com/galaxyproject/galaxy/compare/566acab16e52...990501d2d947

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[galaxyproject/galaxy] 9a9d19: Refactored line lengths
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9a9d193eace1646c7dc0e74991ddc14ebd18c37d https://github.com/galaxyproject/galaxy/commit/9a9d193eace1646c7dc0e74991dd… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Refactored line lengths Fixed sorting bug in workflows per user sorting Commit: c057bfa1d8fe4c921e80260f5205fe35f5d1e8b8 https://github.com/galaxyproject/galaxy/commit/c057bfa1d8fe4c921e80260f5205… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-31 (Mon, 31 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/users_last_access_date.mako Log Message: ----------- Fixed format issue in date of last login page Commit: f48dd9942567b23326227b2538d350cd4c118ba3 https://github.com/galaxyproject/galaxy/commit/f48dd9942567b23326227b2538d3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/style/less/reports.less M static/style/blue/base.css M static/style/blue/reports.css M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_date.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/reports/system.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako Log Message: ----------- Merge pull request #678 from Airistotal/dev Reports Refactoring Compare: https://github.com/galaxyproject/galaxy/compare/291d16f3fcf7...f48dd9942567

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[galaxyproject/galaxy] 6273fa: Use standard Galaxy message box styles on tool hel...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6273fa8a5da7bae8c4f4cdda281cc096ee21f70a https://github.com/galaxyproject/galaxy/commit/6273fa8a5da7bae8c4f4cdda281c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Use standard Galaxy message box styles on tool help texts that use rST admonitions. Commit: 291d16f3fcf7f4b7c70f47aa568a08f60262a806 https://github.com/galaxyproject/galaxy/commit/291d16f3fcf7f4b7c70f47aa568a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge pull request #685 from natefoo/help-message-css Use standard Galaxy message box styles on tool help texts that use rST admonitions Compare: https://github.com/galaxyproject/galaxy/compare/e584a3527323...291d16f3fcf7

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[galaxyproject/galaxy] ee4694: Fix issue #525. Repo info dicts and tsr_ids were f...
by GitHub 02 Sep '15

02 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ee46947c3d58a98d0c6640ba3eea3ef405d8c9c3 https://github.com/galaxyproject/galaxy/commit/ee46947c3d58a98d0c6640ba3eea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-installed tools, but the unfiltered info_dict was passed on, causing misalignment of repository and tsr_id. Commit: e584a3527323a0b801e50a86f6fc2032d84b06ed https://github.com/galaxyproject/galaxy/commit/e584a3527323a0b801e50a86f6fc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #681 from mvdbeek/dev Fix issue #525. Repo info dicts and tsr_ids were filtered for pre-ins… Compare: https://github.com/galaxyproject/galaxy/compare/d00b5507c0d3...e584a3527323

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[galaxyproject/usegalaxy-playbook] d1ea56: Dropped FROG; added Whale Shark to slide rotation.
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d1ea56bcd75e1dd116cb40e1e05466b32bb0498e https://github.com/galaxyproject/usegalaxy-playbook/commit/d1ea56bcd75e1dd1… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: A files/galaxy/common/static/welcome_img/WhaleSharkGalaxy.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped FROG; added Whale Shark to slide rotation.

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[galaxyproject/usegalaxy-playbook] 39697f: Send user emails to Pulsar
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 39697f3e0ace753a5eed10d3a47ed58290f5ed34 https://github.com/galaxyproject/usegalaxy-playbook/commit/39697f3e0ace753a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Send user emails to Pulsar

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[galaxyproject/usegalaxy-playbook] 6f88ff: Update Main Pulsar, so we can use the queued_drmaa...
by GitHub 01 Sep '15

01 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f88ffbe73cf9c28f3bfadf2853a64aad527e1a6 https://github.com/galaxyproject/usegalaxy-playbook/commit/6f88ffbe73cf9c28… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M production/group_vars/pulsarservers.yml M production/host_vars/login5.stampede.tacc.utexas.edu.yml A production/secret_host_vars/default.yml A production/secret_host_vars/login5.stampede.tacc.utexas.edu.yml R production/secret_vars/pulsarservers.yml Log Message: ----------- Update Main Pulsar, so we can use the queued_drmaa_xsede manager.

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