- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] ef9362: Fix pretty_print_time_interval for MySQL. Fix #161...
by GitHub 19 Feb '16

19 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: ef9362971920c6561015376d3f604bf6234f2547 https://github.com/galaxyproject/galaxy/commit/ef9362971920c6561015376d3f60… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix pretty_print_time_interval for MySQL. Fix #1619. Commit: 6c83fbe24dd0dea35967021c061e975225aeb02b https://github.com/galaxyproject/galaxy/commit/6c83fbe24dd0dea35967021c061e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1761 from nsoranzo/release_15.10_fix_for_1619 [15.10] Fix pretty_print_time_interval for MySQL. Commit: b5e91d23779cc6db491b7d7b1701b25cb10da6fb https://github.com/galaxyproject/galaxy/commit/b5e91d23779cc6db491b7d7b1701… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/util/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/b4c823f2cd47...b5e91d23779c

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[galaxyproject/galaxy] 7b8f67: Place logo into config, add masthead test cases
by GitHub 19 Feb '16

19 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7b8f6751720a2caaa5b13f7089d1aa1c98fbedf6 https://github.com/galaxyproject/galaxy/commit/7b8f6751720a2caaa5b13f7089d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M lib/galaxy/managers/configuration.py M static/maps/layout/masthead.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/masthead.js M templates/webapps/galaxy/galaxy.masthead.mako M test/qunit/tests/masthead_tests.js Log Message: ----------- Place logo into config, add masthead test cases Commit: 580895af1d642a52559e0bfa1788808a7c790b05 https://github.com/galaxyproject/galaxy/commit/580895af1d642a52559e0bfa1788… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M static/maps/mvc/workflow/workflow-view-node.js.map M static/scripts/mvc/workflow/workflow-view-node.js Log Message: ----------- Revision Commit: 7ea4668ff732f22c0d686ed35fd6ff1a0c431736 https://github.com/galaxyproject/galaxy/commit/7ea4668ff732f22c0d686ed35fd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/utils/utils.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/modules.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.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/form/form-section.js M static/scripts/utils/utils.js M test/qunit/tests/masthead_tests.js Log Message: ----------- Remove former populate_state Commit: 032ecd1e6edc8075de5b3ad0c7a815b46099a1de https://github.com/galaxyproject/galaxy/commit/032ecd1e6edc8075de5b3ad0c7a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Remove former update state Commit: 25c6eda06e75353c904f4e42864b72a30e35df62 https://github.com/galaxyproject/galaxy/commit/25c6eda06e75353c904f4e42864b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove regular tool handling from editor_form_post Commit: 89759a00c15e567e6e01ba47d28237d62605aaaa https://github.com/galaxyproject/galaxy/commit/89759a00c15e567e6e01ba47d282… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Remove DummyDataset Commit: 6ffa104cb3931a60a484a4a42808e57a64dfbdd6 https://github.com/galaxyproject/galaxy/commit/6ffa104cb3931a60a484a4a42808… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/form_builder.py M lib/galaxy/workflow/modules.py Log Message: ----------- Use visit inputs to set runtime config, remove conflicting booleans Commit: 9423283e83f756f79dd6167c39c47a38557075a0 https://github.com/galaxyproject/galaxy/commit/9423283e83f756f79dd6167c39c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix ftp handling Commit: 664ae0c8dfa61fac9147675d6da2a32128ea7136 https://github.com/galaxyproject/galaxy/commit/664ae0c8dfa61fac9147675d6da2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/workflow_util.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M test/api/test_tools.py M test/unit/tools/test_execution.py Log Message: ----------- Attempt to strip legacy collection handling, fixes Commit: 5a8246878473b988a163606d21bbd6b5ab0edaf4 https://github.com/galaxyproject/galaxy/commit/5a8246878473b988a163606d21bb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use regular dataset matching for selected values Commit: 5041c80d85ba5686f3d5f815349263ed4f8f0150 https://github.com/galaxyproject/galaxy/commit/5041c80d85ba5686f3d5f8153492… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Fix optional column parameter handling and accept_default tag Commit: 5ff028a9d0636e1e7f0e4bab02d40c98666a4ed8 https://github.com/galaxyproject/galaxy/commit/5ff028a9d0636e1e7f0e4bab02d4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/utils/utils.js M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/workflow_util.py M static/maps/layout/masthead.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/workflow/workflow-view-node.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/layout/masthead.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/utils/utils.js M templates/webapps/galaxy/galaxy.masthead.mako M test/api/test_tools.py M test/qunit/tests/masthead_tests.js M test/unit/tools/test_column_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py Log Message: ----------- Merge pull request #1711 from guerler/revise_states_000 Revise tool parameter handling, remove redundancies Compare: https://github.com/galaxyproject/galaxy/compare/a0537762f286...5ff028a9d063

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[galaxyproject/galaxy] ef9362: Fix pretty_print_time_interval for MySQL. Fix #161...
by GitHub 19 Feb '16

19 Feb '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: ef9362971920c6561015376d3f604bf6234f2547 https://github.com/galaxyproject/galaxy/commit/ef9362971920c6561015376d3f60… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix pretty_print_time_interval for MySQL. Fix #1619. Commit: 6c83fbe24dd0dea35967021c061e975225aeb02b https://github.com/galaxyproject/galaxy/commit/6c83fbe24dd0dea35967021c061e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1761 from nsoranzo/release_15.10_fix_for_1619 [15.10] Fix pretty_print_time_interval for MySQL. Compare: https://github.com/galaxyproject/galaxy/compare/476734d86510...6c83fbe24dd0

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[galaxyproject/galaxy] 4c0993: Fix updating in-memory tools for tool shed install...
by GitHub 19 Feb '16

19 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4c0993cc420bc5e6a1d315677962d41803a41cd3 https://github.com/galaxyproject/galaxy/commit/4c0993cc420bc5e6a1d315677962… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix updating in-memory tools for tool shed installs into sections. Commit: b4c823f2cd47bd0f75351c820651abfefa1a8472 https://github.com/galaxyproject/galaxy/commit/b4c823f2cd47bd0f75351c820651… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1758 from jmchilton/ts_section_fix [16.01] Fix updating in-memory tools for tool shed installs into sections. Compare: https://github.com/galaxyproject/galaxy/compare/3f34131ff506...b4c823f2cd47

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[galaxyproject/galaxy] aad5d9: Bump 15.10 version to 15.10.1 (and apparently it h...
by GitHub 19 Feb '16

19 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aad5d9a2e557e935bd88f725deb10d0ed82468d8 https://github.com/galaxyproject/galaxy/commit/aad5d9a2e557e935bd88f725deb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump 15.10 version to 15.10.1 (and apparently it has been incorrectly set to 15.10.dev all this time). Commit: 868acc362f6ce8a8b3559fcb88ebb4c060321905 https://github.com/galaxyproject/galaxy/commit/868acc362f6ce8a8b3559fcb88eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1555 from natefoo/release_15.10 [15.10] Bump 15.10 version to 15.10.1 Commit: 37b98b773ea378bdd4a7845d60f589f7454f2291 https://github.com/galaxyproject/galaxy/commit/37b98b773ea378bdd4a7845d60f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Load whitelist regardless of whether the setting is explicit in config. This is a sensible enough default, and requiring the option to be set in galaxy.ini is cumbersome and unnecessary since it's admin-only functionality. Commit: aabc916ed20ac7f25174ce4d552b735253697081 https://github.com/galaxyproject/galaxy/commit/aabc916ed20ac7f25174ce4d552b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1749 from dannon/whitelist_loading Load whitelist regardless of whether the setting is explicit in config. Commit: 84de6b4ed31906756c3c219eda3f4462773d0a21 https://github.com/galaxyproject/galaxy/commit/84de6b4ed31906756c3c219eda3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.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/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Fix target or window.location when importing histories from display.mako (shared with me->view) to allow for iframes; silence popup-menu.js when menu is closed due to location change Commit: 80a858a3afd970ca086992744b46725eb829b94e https://github.com/galaxyproject/galaxy/commit/80a858a3afd970ca086992744b46… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.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/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge pull request #1753 from carlfeberhard/release_16.01 [16.01] Fix target or window.location when importing histories from display.m… Commit: 587d450402f8b618e4922a04aa87fc5625edce82 https://github.com/galaxyproject/galaxy/commit/587d450402f8b618e4922a04aa87… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. Commit: 476734d8651009e38505408be2e5f7331800680b https://github.com/galaxyproject/galaxy/commit/476734d8651009e38505408be2e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge pull request #1759 from nsoranzo/release_15.10_fix_for_1702 [15.10] Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Commit: 3f34131ff506836d400f8d55b696d8044546b162 https://github.com/galaxyproject/galaxy/commit/3f34131ff506836d400f8d55b696… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/version.py Commit: a0537762f2861247109ead028c33eaca2bd42dbc https://github.com/galaxyproject/galaxy/commit/a0537762f2861247109ead028c33… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M lib/galaxy/config.py M lib/tool_shed/util/encoding_util.py M static/maps/mvc/ui/popup-menu.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/ui/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge branch 'release_16.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/68e6312a6410...a0537762f286

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[galaxyproject/galaxy] aad5d9: Bump 15.10 version to 15.10.1 (and apparently it h...
by GitHub 19 Feb '16

19 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: aad5d9a2e557e935bd88f725deb10d0ed82468d8 https://github.com/galaxyproject/galaxy/commit/aad5d9a2e557e935bd88f725deb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump 15.10 version to 15.10.1 (and apparently it has been incorrectly set to 15.10.dev all this time). Commit: 868acc362f6ce8a8b3559fcb88ebb4c060321905 https://github.com/galaxyproject/galaxy/commit/868acc362f6ce8a8b3559fcb88eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1555 from natefoo/release_15.10 [15.10] Bump 15.10 version to 15.10.1 Commit: 587d450402f8b618e4922a04aa87fc5625edce82 https://github.com/galaxyproject/galaxy/commit/587d450402f8b618e4922a04aa87… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. Commit: 476734d8651009e38505408be2e5f7331800680b https://github.com/galaxyproject/galaxy/commit/476734d8651009e38505408be2e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge pull request #1759 from nsoranzo/release_15.10_fix_for_1702 [15.10] Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Commit: 3f34131ff506836d400f8d55b696d8044546b162 https://github.com/galaxyproject/galaxy/commit/3f34131ff506836d400f8d55b696… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge branch 'release_15.10' into release_16.01 Conflicts: lib/galaxy/version.py Compare: https://github.com/galaxyproject/galaxy/compare/80a858a3afd9...3f34131ff506

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[galaxyproject/galaxy] 587d45: Fix installation of Tool Shed repositories contain...
by GitHub 19 Feb '16

19 Feb '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 587d450402f8b618e4922a04aa87fc5625edce82 https://github.com/galaxyproject/galaxy/commit/587d450402f8b618e4922a04aa87… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. Commit: 476734d8651009e38505408be2e5f7331800680b https://github.com/galaxyproject/galaxy/commit/476734d8651009e38505408be2e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/tool_shed/util/encoding_util.py Log Message: ----------- Merge pull request #1759 from nsoranzo/release_15.10_fix_for_1702 [15.10] Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Compare: https://github.com/galaxyproject/galaxy/compare/868acc362f6c...476734d86510

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[galaxyproject/usegalaxy-playbook] c9696f: install new MEME and bwa on Main
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c9696f8218c4e21051ae7e59daec2140dddd161e https://github.com/galaxyproject/usegalaxy-playbook/commit/c9696f8218c4e210… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- install new MEME and bwa on Main update Main mutable confs

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[galaxyproject/galaxy] afb2ea: Clean up some twilltestcase methods.
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: afb2ea387d5a8c5b6794f3bf95940cce842aea2b https://github.com/galaxyproject/galaxy/commit/afb2ea387d5a8c5b6794f3bf9594… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M test/base/twilltestcase.py M test/functional/test_admin_features.py M test/functional/test_data_security.py M test/functional/test_dataset_features.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_tags.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py M test/tool_shed/functional/test_1085_repository_dependency_handling.py M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_1130_datatype_converters.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional/test_1150_prior_installation_required.py M test/tool_shed/functional/test_1160_circular_prior_installation_required.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py Log Message: ----------- Clean up some twilltestcase methods. Commit: b96bc82db610a58f2c3fabdd65fc2e99a42b6e45 https://github.com/galaxyproject/galaxy/commit/b96bc82db610a58f2c3fabdd65fc… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M test/functional/test_get_data.py M test/tool_shed/functional/test_1170_complex_prior_installation_required.py Log Message: ----------- Fix overly enthusiastic s///g. Commit: a941e88b04005f8f44338af65ee2212447181da7 https://github.com/galaxyproject/galaxy/commit/a941e88b04005f8f44338af65ee2… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: R test/tool_shed/functional/test_1085_repository_dependency_handling.py R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py A test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1130_datatype_converters.py A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1140_tool_help_images.py A test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1150_prior_installation_required.py R test/tool_shed/functional/test_1160_circular_prior_installation_required.py A test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_complex_prior_installation_required.py A test/tool_shed/functional/test_1170_prior_installation_required.py A test/tool_shed/functional/test_1180_circular_prior_installation_required.py A test/tool_shed/functional/test_1190_complex_prior_installation_required.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py Log Message: ----------- Ensure that a valid login exists after cookies are cleared. Commit: 68e6312a6410b44edd7f52d629f422a62d2818ce https://github.com/galaxyproject/galaxy/commit/68e6312a6410b44edd7f52d629f4… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M test/base/twilltestcase.py M test/functional/test_admin_features.py M test/functional/test_data_security.py M test/functional/test_dataset_features.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_tags.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1085_repository_dependency_handling.py R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py A test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1130_datatype_converters.py A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1140_tool_help_images.py A test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1150_prior_installation_required.py R test/tool_shed/functional/test_1160_circular_prior_installation_required.py A test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_complex_prior_installation_required.py A test/tool_shed/functional/test_1170_prior_installation_required.py A test/tool_shed/functional/test_1180_circular_prior_installation_required.py A test/tool_shed/functional/test_1190_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py Log Message: ----------- Merge pull request #1742 from davebx/ttc_cleanup Clean up some twilltestcase methods. Compare: https://github.com/galaxyproject/galaxy/compare/f5277a654a04...68e6312a6410

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[galaxyproject/galaxy] 84de6b: Fix target or window.location when importing histo...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 84de6b4ed31906756c3c219eda3f4462773d0a21 https://github.com/galaxyproject/galaxy/commit/84de6b4ed31906756c3c219eda3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.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/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Fix target or window.location when importing histories from display.mako (shared with me->view) to allow for iframes; silence popup-menu.js when menu is closed due to location change Commit: 80a858a3afd970ca086992744b46725eb829b94e https://github.com/galaxyproject/galaxy/commit/80a858a3afd970ca086992744b46… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M static/maps/mvc/ui/popup-menu.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/popup-menu.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge pull request #1753 from carlfeberhard/release_16.01 [16.01] Fix target or window.location when importing histories from display.m… Compare: https://github.com/galaxyproject/galaxy/compare/aabc916ed20a...80a858a3afd9

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