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

[galaxyproject/galaxy] 36d951: More Python 3 fixes.
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 36d9514e26037a927ad8becab9a834a4807abc50 https://github.com/galaxyproject/galaxy/commit/36d9514e26037a927ad8becab9a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-20 (Sun, 20 Dec 2015) Changed paths: M lib/galaxy/objectstore/pulsar.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/expressions.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/topsort.py M test/unit/test_objectstore.py Log Message: ----------- More Python 3 fixes. This fixes all unit tests for code exclusively covering the stuff I'm moving into the galaxy-lib that will be used by planemo, pulsar, and future tooling efforts. Commit: ae2b94824a322909fb29277ea2571c419d09946b https://github.com/galaxyproject/galaxy/commit/ae2b94824a322909fb29277ea257… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M lib/galaxy/objectstore/pulsar.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/expressions.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/topsort.py M test/unit/test_objectstore.py Log Message: ----------- Merge pull request #1376 from jmchilton/py3_0 More Python 3 fixes. Compare: https://github.com/galaxyproject/galaxy/compare/6eb8eae3967d...ae2b94824a32

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[galaxyproject/usegalaxy-playbook] 806c37: update Main mutable confs
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 806c37931bcf518cb47e7ddffb032219930cbb10 https://github.com/galaxyproject/usegalaxy-playbook/commit/806c37931bcf518c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- update Main mutable confs

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[galaxyproject/usegalaxy-playbook] a4cdf9: Mutable configs on Test
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a4cdf9891378d5e8f984c3429343f3a6328a989e https://github.com/galaxyproject/usegalaxy-playbook/commit/a4cdf9891378d5e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Mutable configs on Test Commit: 7210287035d0a1a969e975d02acbe74cce2e8e07 https://github.com/galaxyproject/usegalaxy-playbook/commit/7210287035d0a1a9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Fix two bugs with dynamic resource selection on Test: 1. Users could not use the team destination if they were also in the reserved partition user list. 2. align_families was submitting to the wrong destination. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/034fd45e74c7...…

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[galaxyproject/usegalaxy-playbook] 034fd4: update MTS
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 034fd45e74c713a9e438578a07badacc57d261b2 https://github.com/galaxyproject/usegalaxy-playbook/commit/034fd45e74c713a9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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[galaxyproject/galaxy] 048561: Avoid duplicate upload entries, revise modals, add...
by GitHub 20 Dec '15

20 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 048561d282d32373e4432edcccb54fe963eb6f95 https://github.com/galaxyproject/galaxy/commit/048561d282d32373e4432edcccb5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-19 (Sat, 19 Dec 2015) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M static/maps/layout/page.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/utils/uploadbox.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/page.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/qunit/test-app.js A test/qunit/tests/modal_dialog_tests.html A test/qunit/tests/modal_dialog_tests.js Log Message: ----------- Avoid duplicate upload entries, revise modals, add tests Revise styles Add more tests Commit: 39e7f025ebd9386f5b07ca99f3b233cd94299c32 https://github.com/galaxyproject/galaxy/commit/39e7f025ebd9386f5b07ca99f3b2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-19 (Sat, 19 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.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/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js R test/qunit/tests/modal_dialog_tests.html R test/qunit/tests/modal_dialog_tests.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js Log Message: ----------- Refine popover wrapper Revise popover, add tests Commit: 17d733b0428f125e6deb1007937dff6b9bfe80b2 https://github.com/galaxyproject/galaxy/commit/17d733b0428f125e6deb1007937d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-19 (Sat, 19 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- Move closing events to show/hide function Commit: 6eb8eae3967d62909f2b4d5fcded46f5ea411b40 https://github.com/galaxyproject/galaxy/commit/6eb8eae3967d62909f2b4d5fcded… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-20 (Sun, 20 Dec 2015) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M static/maps/layout/page.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/utils/uploadbox.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/page.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/qunit/test-app.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js Log Message: ----------- Merge pull request #1377 from guerler/revise_upload_000 Uploader enhancements, modal and popover cleanup, fixes and new test cases Compare: https://github.com/galaxyproject/galaxy/compare/6678544caa7b...6eb8eae3967d

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[galaxyproject/usegalaxy-playbook] 17d228: update Main tool sections
by GitHub 19 Dec '15

19 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 17d22827563678d66476b3c73908fb9f7be9d799 https://github.com/galaxyproject/usegalaxy-playbook/commit/17d22827563678d6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- update Main tool sections

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[galaxyproject/usegalaxy-playbook] 4227c6: move Main tools to correct sections
by GitHub 19 Dec '15

19 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4227c69089029792eca27f66d3dfb0df9db407fc https://github.com/galaxyproject/usegalaxy-playbook/commit/4227c69089029792… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml Log Message: ----------- move Main tools to correct sections no idea why it got added to the migrated_tool_conf, weird

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[galaxyproject/usegalaxy-playbook] 98e6ac: install bedtools to Main
by GitHub 19 Dec '15

19 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 98e6ac64a63378007cf7540d1871d0c7df321714 https://github.com/galaxyproject/usegalaxy-playbook/commit/98e6ac64a6337800… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- install bedtools to Main

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[galaxyproject/usegalaxy-playbook] 60298c: install new tools on Main
by GitHub 19 Dec '15

19 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 60298c0f0ca6416439542fce16b28b2d3724ac1a https://github.com/galaxyproject/usegalaxy-playbook/commit/60298c0f0ca64164… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- install new tools on Main

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[galaxyproject/usegalaxy-playbook] d24608: install new trimmers to Main
by GitHub 18 Dec '15

18 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d24608b54bfb25dcf179d80e685b372b571c902f https://github.com/galaxyproject/usegalaxy-playbook/commit/d24608b54bfb25dc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- install new trimmers to Main

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