- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 74d8fa: Change 'History Actions' to 'Current History' in h...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 74d8faac9f07407ac9df344a78c9ecb06c178f93 https://github.com/galaxyproject/galaxy/commit/74d8faac9f07407ac9df344a78c9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js 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/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Change 'History Actions' to 'Current History' in history options menu. as it was before 1cc57b1eb2c295dbd68837c864740b6ff079b83d. Commit: ec08ec60bb4dadaf6f8759f9dce79f764f26c909 https://github.com/galaxyproject/galaxy/commit/ec08ec60bb4dadaf6f8759f9dce7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js 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/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3205 from blankenberg/history-current-options-name_16.10 [16.10] Change 'History Actions' to 'Current History' in history options menu. Compare: https://github.com/galaxyproject/galaxy/compare/aadc14d967c3...ec08ec60bb4d

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[galaxyproject/usegalaxy-playbook] 74f97c: First pass at a uWSGI zerg mode setup. Requires th...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 74f97c6ac5b03d254759e2f5582d28348ad7f9e4 https://github.com/galaxyproject/usegalaxy-playbook/commit/74f97c6ac5b03d25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 M templates/supervisor/galaxy.j2 Log Message: ----------- First pass at a uWSGI zerg mode setup. Requires the uWSGI author's one-off spinningfifo plugin from an email and has a bad race condition encountered when starting zerglings simultaneously: Both will attempt to write `2p` to the running fifo at the same time and both will attempt to grab the `new` fifo at the same time, and one or both will end up in the running state, unpaused. Staggering starting/restarting can be used to solve this but hopefully I can come up with a better solution. uWSGI/server full restarts will need to be hand-held for now. But `galaxy graceful` and the new `galaxy gracefuluwsgi` work very nice.

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[galaxyproject/usegalaxy-playbook] 70201c: Take down downtime message
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 70201ca9de45477f2a7c082fce3d4799580c0ff0 https://github.com/galaxyproject/usegalaxy-playbook/commit/70201ca9de45477f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Take down downtime message

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[galaxyproject/galaxy] 6fd58a: Merge pull request #3191 from dannon/version-16.10
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6fd58afa6daf708f373513782ac907c154c266da https://github.com/galaxyproject/galaxy/commit/6fd58afa6daf708f373513782ac9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3191 from dannon/version-16.10 Update version to 16.10.rc1 Commit: 5c4ac18b44263df72b25826c03d8c2509ca68a1a https://github.com/galaxyproject/galaxy/commit/5c4ac18b44263df72b25826c03d8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.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/tool/tools.js Log Message: ----------- remove unused override this caused Help/Search to point at /root/tool_search Commit: 3f27777e76086ac94c95003882bb82003c277b4e https://github.com/galaxyproject/galaxy/commit/3f27777e76086ac94c95003882bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.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/tool/tools.js Log Message: ----------- Merge pull request #3198 from martenson/fix-search-config [16.10] remove unused (and unintended) config override Commit: 548d3e6f05b722301deefada71d5dafda81a1881 https://github.com/galaxyproject/galaxy/commit/548d3e6f05b722301deefada71d5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Fixes for deleting histories broken in 1cc57b1eb2c295dbd68837c864740b6ff079b83d Commit: 5ba820116365ad42dd24e099b747b40d399e6dee https://github.com/galaxyproject/galaxy/commit/5ba820116365ad42dd24e099b747… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M static/maps/mvc/history/options-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/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Pack scripts Commit: aadc14d967c30683a10e68df61b82bb4f805de98 https://github.com/galaxyproject/galaxy/commit/aadc14d967c30683a10e68df61b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-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/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3203 from blankenberg/fix_history_delete_16.10 [16.10] Fixes for deleting histories Commit: d2c95b43fa33f9f4b14d274ffa60beb03a80fbb6 https://github.com/galaxyproject/galaxy/commit/d2c95b43fa33f9f4b14d274ffa60… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tools.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/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tools.js Log Message: ----------- Merge pull request #3204 from galaxyproject/release_16.10 Merge release_16.10 into dev Compare: https://github.com/galaxyproject/galaxy/compare/78b533d1b544...d2c95b43fa33

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[galaxyproject/galaxy] 548d3e: Fixes for deleting histories broken in 1cc57b1eb2c...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 548d3e6f05b722301deefada71d5dafda81a1881 https://github.com/galaxyproject/galaxy/commit/548d3e6f05b722301deefada71d5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Fixes for deleting histories broken in 1cc57b1eb2c295dbd68837c864740b6ff079b83d Commit: 5ba820116365ad42dd24e099b747b40d399e6dee https://github.com/galaxyproject/galaxy/commit/5ba820116365ad42dd24e099b747… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M static/maps/mvc/history/options-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/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Pack scripts Commit: aadc14d967c30683a10e68df61b82bb4f805de98 https://github.com/galaxyproject/galaxy/commit/aadc14d967c30683a10e68df61b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-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/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3203 from blankenberg/fix_history_delete_16.10 [16.10] Fixes for deleting histories Compare: https://github.com/galaxyproject/galaxy/compare/3f27777e7608...aadc14d967c3

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[galaxyproject/galaxy] c0a7fa: Don't load tools from paths that start with `.` or...
by GitHub 21 Nov '16

21 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0a7fabc354598b1a40ea87291c28f70127db357 https://github.com/galaxyproject/galaxy/commit/c0a7fabc354598b1a40ea87291c2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Don't load tools from paths that start with `.` or `_` Commit: 78b533d1b5445c843090ec42c134d2fa335134a3 https://github.com/galaxyproject/galaxy/commit/78b533d1b5445c843090ec42c134… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3201 from mvdbeek/do_not_load_tools_from_hidden_paths Don't load tools from paths that start with `.` or `_` Compare: https://github.com/galaxyproject/galaxy/compare/52c8e495dc17...78b533d1b544

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[galaxyproject/galaxy] 3ea730: Fix table
by GitHub 19 Nov '16

19 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3ea730f734c71e5e3aa182c96f7be81850ee8527 https://github.com/galaxyproject/galaxy/commit/3ea730f734c71e5e3aa182c96f7b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M templates/webapps/galaxy/user/list_users.mako Log Message: ----------- Fix table Commit: 52c8e495dc1746e4280c7d6837dd590f9b98566e https://github.com/galaxyproject/galaxy/commit/52c8e495dc1746e4280c7d6837dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-19 (Sat, 19 Nov 2016) Changed paths: M templates/webapps/galaxy/user/list_users.mako Log Message: ----------- Merge pull request #3200 from erasche/user-info-page Fix table Compare: https://github.com/galaxyproject/galaxy/compare/33894ca744be...52c8e495dc17

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[galaxyproject/usegalaxy-playbook] 924a93: *sigh*
by GitHub 18 Nov '16

18 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 924a931311400fde319679c3f9901fa404cf6114 https://github.com/galaxyproject/usegalaxy-playbook/commit/924a931311400fde… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- *sigh*

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[galaxyproject/usegalaxy-playbook] 2b3d45: Mutable configs
by GitHub 18 Nov '16

18 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2b3d45fc7b0c1b55b35629eb39a003d68e350947 https://github.com/galaxyproject/usegalaxy-playbook/commit/2b3d45fc7b0c1b55… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- Mutable configs

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[galaxyproject/usegalaxy-playbook] 94ade5: Downtime message
by GitHub 18 Nov '16

18 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 94ade57d02e4430ef1173fcc42027d5e63752469 https://github.com/galaxyproject/usegalaxy-playbook/commit/94ade57d02e4430e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Downtime message

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[galaxyproject/galaxy] 5c4ac1: remove unused override
by GitHub 18 Nov '16

18 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 5c4ac18b44263df72b25826c03d8c2509ca68a1a https://github.com/galaxyproject/galaxy/commit/5c4ac18b44263df72b25826c03d8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.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/tool/tools.js Log Message: ----------- remove unused override this caused Help/Search to point at /root/tool_search Commit: 3f27777e76086ac94c95003882bb82003c277b4e https://github.com/galaxyproject/galaxy/commit/3f27777e76086ac94c95003882bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/tool/tools.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/tool/tools.js Log Message: ----------- Merge pull request #3198 from martenson/fix-search-config [16.10] remove unused (and unintended) config override Compare: https://github.com/galaxyproject/galaxy/compare/6fd58afa6daf...3f27777e7608

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[galaxyproject/ansible-galaxy] 19535b: Drop support for "Galaxy pip"
by GitHub 18 Nov '16

18 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 19535b56292b72d38fcc1cf89580a1dd27c0f040 https://github.com/galaxyproject/ansible-galaxy/commit/19535b56292b72d38fcc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- Drop support for "Galaxy pip"

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[galaxyproject/galaxy] a20952: Large cleanup of unused methods from twilltestcase...
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a209523639a822dc546b9d2d946e6199df172368 https://github.com/galaxyproject/galaxy/commit/a209523639a822dc546b9d2d946e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/twilltestcase.py M test/functional/test_library_templates.py Log Message: ----------- Large cleanup of unused methods from twilltestcase. In addition to deleting unused methods, this also moves ones only used by test_library_templates into that file. Commit: 2bf1cf50a37d5295425798374959fbda0257b609 https://github.com/galaxyproject/galaxy/commit/2bf1cf50a37d5295425798374959… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/twilltestcase.py M test/functional/test_library_templates.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Reduce requirements for using get_filename in TwillTestCase. Do not use a self.tool_shed_test_file and make self.shed_tools_dict optional. Commit: b83cfe434ad875744d11d7516dc9cc11dfdec419 https://github.com/galaxyproject/galaxy/commit/b83cfe434ad875744d11d7516dc9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py Log Message: ----------- Refactor generic FunctionalTestCase from TwillTestCase. ApiTestCase uses this newer, smaller base class since these tests do not depend on Twill. Commit: 33894ca744be3fa2eebab6942832f2931d5f0bec https://github.com/galaxyproject/galaxy/commit/33894ca744be3fa2eebab6942832… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py M test/functional/test_library_templates.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #3190 from jmchilton/test_cleanup Various Test Cleanups and Refactorings Compare: https://github.com/galaxyproject/galaxy/compare/50f5c15f63a3...33894ca744be

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[galaxyproject/usegalaxy-playbook] 1325e6: add missing configs to Test also
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1325e6f41c681247b41d06fc47b00ccd20ae5f3c https://github.com/galaxyproject/usegalaxy-playbook/commit/1325e6f41c681247… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- add missing configs to Test also

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[galaxyproject/usegalaxy-playbook] bd61ac: add missing config options
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bd61acefe2c0bb525890fce3f66786b7a1a7ba6b https://github.com/galaxyproject/usegalaxy-playbook/commit/bd61acefe2c0bb52… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- add missing config options spotted by @tnatbaf

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[galaxyproject/galaxy] 9d45f1: Update version to 16.10.rc1
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d45f1e48a4321d5df0543bcfcf2994affa35612 https://github.com/galaxyproject/galaxy/commit/9d45f1e48a4321d5df0543bcfcf2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.10.rc1 Commit: e5b56f102ae003707ad97d9fbb75270543397921 https://github.com/galaxyproject/galaxy/commit/e5b56f102ae003707ad97d9fbb75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01.dev Commit: 3dd28291c339d4ca1f2b165ed6cb2c9d82a7cdd9 https://github.com/galaxyproject/galaxy/commit/3dd28291c339d4ca1f2b165ed6cb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Log Message: ----------- Merge branch 'version-16.10' into version-17.01.dev Commit: 50f5c15f63a388466f8e77437226a93405baa382 https://github.com/galaxyproject/galaxy/commit/50f5c15f63a388466f8e77437226… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3192 from dannon/version-17.01.dev Version 17.01.dev Compare: https://github.com/galaxyproject/galaxy/compare/d8c75e2dffbf...50f5c15f63a3

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[galaxyproject/galaxy] 9d45f1: Update version to 16.10.rc1
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 9d45f1e48a4321d5df0543bcfcf2994affa35612 https://github.com/galaxyproject/galaxy/commit/9d45f1e48a4321d5df0543bcfcf2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.10.rc1 Commit: 6fd58afa6daf708f373513782ac907c154c266da https://github.com/galaxyproject/galaxy/commit/6fd58afa6daf708f373513782ac9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3191 from dannon/version-16.10 Update version to 16.10.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/d8c75e2dffbf...6fd58afa6daf

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[galaxyproject/galaxy]
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 953ee3: change parameters to samtools sort command (new sa...
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 953ee3259999f774887e97d5e72bccb1102540f5 https://github.com/galaxyproject/galaxy/commit/953ee3259999f774887e97d5e72b… Author: Ignacio <ignacio.eguinoa(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- change parameters to samtools sort command (new samtools vers) Commit: 5bb86a3b687732913dee746732060f973b622cff https://github.com/galaxyproject/galaxy/commit/5bb86a3b687732913dee74673206… Author: Ignacio <ignacio.eguinoa(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- correct indentation Commit: efde00d80a916afc20869608a7a1922249581a62 https://github.com/galaxyproject/galaxy/commit/efde00d80a916afc20869608a7a1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Handle samtools 0.x Commit: 592f15c7b5da3f962dda9f98cb978e5c5c6b4a1d https://github.com/galaxyproject/galaxy/commit/592f15c7b5da3f962dda9f98cb97… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: A test-data/bam_from_sam.bam A test-data/sam_with_header.sam A test/functional/tools/sam_to_bam.xml Log Message: ----------- Add sam-to-bam conversion test tool Commit: 8ace021c0af79e5d325d6a590f525bce881715f8 https://github.com/galaxyproject/galaxy/commit/8ace021c0af79e5d325d6a590f52… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Single quote variables in sam-to-bam conversion Commit: d8c75e2dffbfa754eda4fae4c6d3365d42278a4c https://github.com/galaxyproject/galaxy/commit/d8c75e2dffbfa754eda4fae4c6d3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py A test-data/bam_from_sam.bam A test-data/sam_with_header.sam A test/functional/tools/sam_to_bam.xml Log Message: ----------- Merge pull request #3187 from mvdbeek/samtools_1_3_fix Make sam to bam converter tool compatible with samtools >= 1.3 Compare: https://github.com/galaxyproject/galaxy/compare/164a0ad20cbb...d8c75e2dffbf

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[galaxyproject/galaxy] 0b395a: Slight clarification of run.sh messaging when usin...
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b395a7fb3aaebf5fa3a0448338df73c8774e388 https://github.com/galaxyproject/galaxy/commit/0b395a7fb3aaebf5fa3a0448338d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Slight clarification of run.sh messaging when using conda. Commit: 164a0ad20cbbd55b40583c633c1c52dde9ecb7ba https://github.com/galaxyproject/galaxy/commit/164a0ad20cbbd55b40583c633c1c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #3188 from dannon/startup_output_tweaks Slight clarification of run.sh messaging when using conda. Compare: https://github.com/galaxyproject/galaxy/compare/92105d99fae6...164a0ad20cbb

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[galaxyproject/galaxy] b97281: Cleanup for 16.10 rstudio
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b97281920b341d141fe0b94ecd5c8ecc5f175454 https://github.com/galaxyproject/galaxy/commit/b97281920b341d141fe0b94ecd5c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Cleanup for 16.10 rstudio Commit: 0aeb9e816a9807117b26691c248483cbad07e16a https://github.com/galaxyproject/galaxy/commit/0aeb9e816a9807117b26691c2484… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Clean up rstudio conf, now working again Commit: 56a8c01fef6c419d3fb23cec85dbac726831d789 https://github.com/galaxyproject/galaxy/commit/56a8c01fef6c419d3fb23cec85db… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample Log Message: ----------- Bump image Commit: 65fe971008967bbf477b578852e004e94657e215 https://github.com/galaxyproject/galaxy/commit/65fe971008967bbf477b578852e0… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- add correct login url Commit: 198c6d92e608ca78454ca9c06dc2bd8865d8387c https://github.com/galaxyproject/galaxy/commit/198c6d92e608ca78454ca9c06dc2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #17 from nturaga/rstudio_mako_url add correct login url Commit: 92105d99fae6ec892f2eb6eb60c31d68196b061a https://github.com/galaxyproject/galaxy/commit/92105d99fae6ec892f2eb6eb60c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #2818 from erasche/rstudio-1610 Return of RStudio Compare: https://github.com/galaxyproject/galaxy/compare/31b73fd5869f...92105d99fae6

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[galaxyproject/galaxy] d48817: Remove redundant .venv activation -- this is handl...
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d48817adb17b914975c26b90a2dd17887b24744b https://github.com/galaxyproject/galaxy/commit/d48817adb17b914975c26b90a2dd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M run.sh Log Message: ----------- Remove redundant .venv activation -- this is handled in common_startup Commit: 72d360e942da2a614b7d74d3238d2ee0791a8141 https://github.com/galaxyproject/galaxy/commit/72d360e942da2a614b7d74d3238d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Change startup logic for .venv sourcing. If a .venv exists, use it. If not, if conda is there, use it. If no conda, create a .venv. Commit: 7f5d9d2fbd745f2099be15de706112717f9e01f6 https://github.com/galaxyproject/galaxy/commit/7f5d9d2fbd745f2099be15de7061… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- More startup logic tweaks, .venv > conda > new_venv Commit: 985bd0dffd779b55813f6dc1c6bae663e959bd9c https://github.com/galaxyproject/galaxy/commit/985bd0dffd779b55813f6dc1c6ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M run.sh Log Message: ----------- Because common_startup is executed and not sourced, this block needs to remain in run.sh Commit: 31b73fd5869f1c3ae968fb29773cf1631a3f5843 https://github.com/galaxyproject/galaxy/commit/31b73fd5869f1c3ae968fb29773c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #3180 from dannon/venv_over_conda Prefer existing .venv over conda, when both are available. Compare: https://github.com/galaxyproject/galaxy/compare/0b8fc7c8cca4...31b73fd5869f

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[galaxyproject/galaxy] 4e6e7d: Validate cycles and step size before building mode...
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e6e7d36f87249b93f4a49249e227409e629305e https://github.com/galaxyproject/galaxy/commit/4e6e7d36f87249b93f4a49249e22… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Validate cycles and step size before building model for workflow execution Commit: 0b8fc7c8cca4b7374f12932b26ef3d854e2d8491 https://github.com/galaxyproject/galaxy/commit/0b8fc7c8cca4b7374f12932b26ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge remote-tracking branch 'guerler/validate_workflow' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e5b69a711d14...0b8fc7c8cca4

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[galaxyproject/galaxy] c5a519: Change wording to be more clear about how workflow...
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5a51967173b7e5b0ecf6bbb1340db9ff54a3aed https://github.com/galaxyproject/galaxy/commit/c5a51967173b7e5b0ecf6bbb1340… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M static/maps/mvc/tool/tool-form-workflow.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/tool/tool-form-workflow.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Change wording to be more clear about how workflow output cleanup works. Also adjust styling so that the rows in the workflow editor box are less smashed together. Commit: 277d3c3e58d28904752674c9210f02b88e481eb7 https://github.com/galaxyproject/galaxy/commit/277d3c3e58d28904752674c9210f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Slight wording tweak. Commit: 8966b741317431275100c24ab3cc69a221de646c https://github.com/galaxyproject/galaxy/commit/8966b741317431275100c24ab3cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M client/galaxy/style/less/ui.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Swap to section row selector Commit: 5028e2a25107e8f4cd2f136ab275853b5e31bb7f https://github.com/galaxyproject/galaxy/commit/5028e2a25107e8f4cd2f136ab275… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CONTRIBUTORS.md M Makefile M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M 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test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M 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tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into workflow_intermediates_ux Commit: e5b69a711d14fa8e8876041f92160db19da3e9bf https://github.com/galaxyproject/galaxy/commit/e5b69a711d14fa8e8876041f9216… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #2966 from dannon/workflow_intermediates_ux Change wording to be more clear about how workflow output cleanup wor… Compare: https://github.com/galaxyproject/galaxy/compare/ac5b7efc5f88...e5b69a711d14

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[galaxyproject/galaxy] fb69af: Update ToolPanelElements instance locally
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb69afae28c434f35860ccaa4591e95fe3acfe91 https://github.com/galaxyproject/galaxy/commit/fb69afae28c434f35860ccaa4591… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update ToolPanelElements instance locally in addition to Galaxy's IPC call via send_control_task. Commit: ac5b7efc5f88da9b337a8d98f36dbdbfe29bb3f6 https://github.com/galaxyproject/galaxy/commit/ac5b7efc5f88da9b337a8d98f36d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3130 from mvdbeek/fix_invalid_section_key Update ToolPanelElements instance locally Compare: https://github.com/galaxyproject/galaxy/compare/2f08dd72c3e0...ac5b7efc5f88

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