Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 92aff618cb435f2b4d5805378e4bbcd67ae1f7a4 https://github.com/galaxyproject/galaxy/commit/92aff618cb435f2b4d5805378e4bb... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py Log Message: ----------- Fix for redirecting a non-user when a tool has require_login=True. Commit: e1d937e430a859997b252432cc1b01a509fc68a0 https://github.com/galaxyproject/galaxy/commit/e1d937e430a859997b252432cc1b0... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py Log Message: ----------- Merge pull request #2180 from blankenberg/tool-login-required [16.04] Fix for redirecting a non-user when a tool has require_login=True. Commit: 49a7328186bff37fc55725eb4b9af8dbda4ecdb6 https://github.com/galaxyproject/galaxy/commit/49a7328186bff37fc55725eb4b9af... Author: John Chilton <jmchilton@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/integration/test_pulsar_embedded.py Log Message: ----------- More Pulsar fixes. - Fix working directory outputs for a2e31403753c407e7f6966b69b157e32f5f3ef8a (giving tools clean working directories). - Fix copy action when target directory doesn't already exist (https://github.com/galaxyproject/pulsar/pull/107 thanks to @natefoo). - Fix handling of Pulsar jobs that fail during submission (https://github.com/galaxyproject/pulsar/pull/103 thanks to @mvdbeek). - Fix PBS status reporting (https://github.com/galaxyproject/pulsar/pull/102 thanks to @mvdbeek). - Fix for JetStream that allows setting staging directories on a per-manager basis (https://github.com/galaxyproject/pulsar/commit/7d4030412d1aa58d0c3daa86d0ad7...). Commit: cea9a12238b681892b8956dd6961383a9a025220 https://github.com/galaxyproject/galaxy/commit/cea9a12238b681892b8956dd69613... Author: guerler <aysam.guerler@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Replace masthead dom to avoid duplication Commit: ab015c67dff7261dfd233901fe6f2ea97db2d727 https://github.com/galaxyproject/galaxy/commit/ab015c67dff7261dfd233901fe6f2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #2182 from guerler/fix_masthead_002 [16.04] Remove redundant ui divs, move masthead into #everything Commit: 7ad55b7eb8ffb49d4cca299432a78b6362207c1d https://github.com/galaxyproject/galaxy/commit/7ad55b7eb8ffb49d4cca299432a78... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- try pushing again when we get unexpected exception... Commit: 76386b5eab770b1f7fdb4afbf776947f8e7359fd https://github.com/galaxyproject/galaxy/commit/76386b5eab770b1f7fdb4afbf7769... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- remove unwanted check Commit: a85b5ee762009a95ff20273ece10bad06d76420b https://github.com/galaxyproject/galaxy/commit/a85b5ee762009a95ff20273ece10b... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- remove unused import Commit: 1fd326855d5b19b9b0fa7b078d26219618823b7f https://github.com/galaxyproject/galaxy/commit/1fd326855d5b19b9b0fa7b078d262... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- improve on refactoring of the test Commit: 53021ef33ea3e024d6a7b775fb1a8df1be29ea54 https://github.com/galaxyproject/galaxy/commit/53021ef33ea3e024d6a7b775fb1a8... Author: John Chilton <jmchilton@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #2186 from martenson/port-tstest-fix [16.04] Port TS push test fix Commit: 9ea399694f2678fe99f14a9fdfd1056cad1759f0 https://github.com/galaxyproject/galaxy/commit/9ea399694f2678fe99f14a9fdfd10... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M templates/display_base.mako M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, display_base: render links in header first This allows text to flow around them and for them to be positioned at/ near the top (and remain clickable). This is a stop-gap/kludge and what we'd really want to do is move away from absolutely positoned panels/layouts so elements like this can stretch more naturally around their contents. Fixes #2172 Commit: 5d39c84a71fdcf0611dd7e480c41ff26d88551a9 https://github.com/galaxyproject/galaxy/commit/5d39c84a71fdcf0611dd7e480c41f... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, history/display: remove unused styles Commit: 980d37f50f324f097ca80b4508265c5160ac7ed0 https://github.com/galaxyproject/galaxy/commit/980d37f50f324f097ca80b4508265... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- fix a bug with missing history_id in libraries dataset import also allow creation of new histories as exists in the folderlist view Commit: 35ab333c7e74275a1b31b49a805036a1e09938ec https://github.com/galaxyproject/galaxy/commit/35ab333c7e74275a1b31b49a80503... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map Log Message: ----------- remove old template Commit: 642fccd288415b36c2e8a1a725191e4480e2d6d9 https://github.com/galaxyproject/galaxy/commit/642fccd288415b36c2e8a1a725191... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- do not pass variable that is not used Commit: bbd76f139b3118f968f68cbc64c02e6ce5b57667 https://github.com/galaxyproject/galaxy/commit/bbd76f139b3118f968f68cbc64c02... Author: guerler <aysam.guerler@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Fix message in legacy panel mako Commit: db805184f5e4683c6529891b5c663bb9b1445d41 https://github.com/galaxyproject/galaxy/commit/db805184f5e4683c6529891b5c663... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M test/integration/test_pulsar_embedded.py Log Message: ----------- Merge pull request #2184 from jmchilton/pulsar_fixes_more_v2_updated_even_more_revised_2 [16.04] More Pulsar fixes. Commit: 76691ab2e1474174670128ab81ba080f68351930 https://github.com/galaxyproject/galaxy/commit/76691ab2e1474174670128ab81ba0... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M templates/display_base.mako M templates/webapps/galaxy/history/display.mako Log Message: ----------- Merge pull request #2189 from carlfeberhard/fix.published-history-long-titles-have-to-be-truncated [16.04] Fix.published history long titles have to be truncated Commit: 75864e552b6a549c045e76a711fc3b1b457c6e5b https://github.com/galaxyproject/galaxy/commit/75864e552b6a549c045e76a711fc3... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Merge pull request #2191 from guerler/fix_message_000 [16.04] Fix message in legacy panel mako Commit: 00a55f8c0285583727155d1b4d397a2b16a4af3c https://github.com/galaxyproject/galaxy/commit/00a55f8c0285583727155d1b4d397... Author: John Chilton <jmchilton@gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- Merge pull request #2190 from martenson/fix-import-libraries [16.04] fix a bug with missing history_id in libraries dataset import Commit: 78f35bfe84391554cfb3fbb05b50334ca7534367 https://github.com/galaxyproject/galaxy/commit/78f35bfe84391554cfb3fbb05b503... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/layout/page.js.map M static/maps/mvc/library/library-dataset-view.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/library/library-dataset-view.js M templates/base/base_panels.mako M templates/display_base.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display.mako M test/integration/test_pulsar_embedded.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f1c008b741cc...78f35bfe8439