April 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e13738: Apply parameter translation for data source tools
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: e13738868519d8c7c6f7dec8cfd598f7929b8828 https://github.com/galaxyproject/galaxy/commit/e13738868519d8c7c6f7dec8cfd5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Apply parameter translation for data source tools Commit: eac0fb9b26c6c52ab695d58cef13c73d3d2566b4 https://github.com/galaxyproject/galaxy/commit/eac0fb9b26c6c52ab695d58cef13… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #2201 from guerler/fix_parameters_000 [16.04] Translate data source tool parameters on parameter expansion Compare: https://github.com/galaxyproject/galaxy/compare/65fa24d57ed8...eac0fb9b26c6

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[galaxyproject/galaxy] b95cca: always fetch new permissions as we are reusing the...
by GitHub 19 Apr '16

19 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b95cca862cae9cf7e78370fd68ea5f530fb8194f https://github.com/galaxyproject/galaxy/commit/b95cca862cae9cf7e78370fd68ea… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- always fetch new permissions as we are reusing the view Commit: e2f88296f8454e9195ad1a6f2d4c9c9ade40ee77 https://github.com/galaxyproject/galaxy/commit/e2f88296f8454e9195ad1a6f2d4c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- Merge pull request #2176 from martenson/fix-permissions-caching [16.01] libraries: always fetch new permissions as we are reusing the view Commit: 212f7f4aabc6e859dfcbe00db2cfa36d4d2e48e8 https://github.com/galaxyproject/galaxy/commit/212f7f4aabc6e859dfcbe00db2cf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: client/galaxy/scripts/mvc/library/library-dataset-view.js static/maps/mvc/library/library-dataset-view.js.map static/maps/mvc/library/library-folder-view.js.map static/maps/mvc/library/library-library-view.js.map static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/library/library-dataset-view.js static/scripts/mvc/library/library-folder-view.js static/scripts/mvc/library/library-library-view.js Commit: cfb8ed32693d6aad0ef26af7af7171e0e8c3ee04 https://github.com/galaxyproject/galaxy/commit/cfb8ed32693d6aad0ef26af7af71… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.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/citation/citation-model.js Log Message: ----------- UI, citations: fix bad merge from 15.10 774487d created a difference between the imported name and the one used. Commit: 3737fc9487ad25ba09960e0d7858d4c15a3087bf https://github.com/galaxyproject/galaxy/commit/3737fc9487ad25ba09960e0d7858… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.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/citation/citation-model.js Log Message: ----------- Merge pull request #2198 from carlfeberhard/fix.citations-again [16.01] UI, citations: fix bad merge from 15.10 Commit: 65fa24d57ed891c312381fd9e7bd5c1872a46a1d https://github.com/galaxyproject/galaxy/commit/65fa24d57ed891c312381fd9e7bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.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/citation/citation-model.js Log Message: ----------- Merge 16.01->16.04, rebuild. Commit: 9b5fdbf9a497b6e7ab10a4910b9929c1a36ff6c1 https://github.com/galaxyproject/galaxy/commit/9b5fdbf9a497b6e7ab10a4910b99… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.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/citation/citation-model.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/78f35bfe8439...9b5fdbf9a497

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[galaxyproject/galaxy] cfb8ed: UI, citations: fix bad merge from 15.10
by GitHub 19 Apr '16

19 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: cfb8ed32693d6aad0ef26af7af7171e0e8c3ee04 https://github.com/galaxyproject/galaxy/commit/cfb8ed32693d6aad0ef26af7af71… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.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/citation/citation-model.js Log Message: ----------- UI, citations: fix bad merge from 15.10 774487d created a difference between the imported name and the one used. Commit: 3737fc9487ad25ba09960e0d7858d4c15a3087bf https://github.com/galaxyproject/galaxy/commit/3737fc9487ad25ba09960e0d7858… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.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/citation/citation-model.js Log Message: ----------- Merge pull request #2198 from carlfeberhard/fix.citations-again [16.01] UI, citations: fix bad merge from 15.10 Commit: 65fa24d57ed891c312381fd9e7bd5c1872a46a1d https://github.com/galaxyproject/galaxy/commit/65fa24d57ed891c312381fd9e7bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.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/citation/citation-model.js Log Message: ----------- Merge 16.01->16.04, rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/212f7f4aabc6...65fa24d57ed8

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[galaxyproject/galaxy] cfb8ed: UI, citations: fix bad merge from 15.10
by GitHub 19 Apr '16

19 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: cfb8ed32693d6aad0ef26af7af7171e0e8c3ee04 https://github.com/galaxyproject/galaxy/commit/cfb8ed32693d6aad0ef26af7af71… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.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/citation/citation-model.js Log Message: ----------- UI, citations: fix bad merge from 15.10 774487d created a difference between the imported name and the one used. Commit: 3737fc9487ad25ba09960e0d7858d4c15a3087bf https://github.com/galaxyproject/galaxy/commit/3737fc9487ad25ba09960e0d7858… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.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/citation/citation-model.js Log Message: ----------- Merge pull request #2198 from carlfeberhard/fix.citations-again [16.01] UI, citations: fix bad merge from 15.10 Compare: https://github.com/galaxyproject/galaxy/compare/e2f88296f845...3737fc9487ad

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[galaxyproject/infrastructure-playbook] d15e8f: Add additional IU Jetstream nodes
by GitHub 19 Apr '16

19 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d15e8f3348f91a488ceecaa724d5e422c1b44bad https://github.com/galaxyproject/infrastructure-playbook/commit/d15e8f3348f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory Log Message: ----------- Add additional IU Jetstream nodes

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[galaxyproject/infrastructure-playbook] d597be: Add new TACC Jetstream instances
by GitHub 19 Apr '16

19 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d597bebd59b07d49b122a903864c3d92a3cf8d54 https://github.com/galaxyproject/infrastructure-playbook/commit/d597bebd59b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Add new TACC Jetstream instances

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[galaxyproject/galaxy] b95cca: always fetch new permissions as we are reusing the...
by GitHub 19 Apr '16

19 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: b95cca862cae9cf7e78370fd68ea5f530fb8194f https://github.com/galaxyproject/galaxy/commit/b95cca862cae9cf7e78370fd68ea… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- always fetch new permissions as we are reusing the view Commit: e2f88296f8454e9195ad1a6f2d4c9c9ade40ee77 https://github.com/galaxyproject/galaxy/commit/e2f88296f8454e9195ad1a6f2d4c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- Merge pull request #2176 from martenson/fix-permissions-caching [16.01] libraries: always fetch new permissions as we are reusing the view Commit: 212f7f4aabc6e859dfcbe00db2cfa36d4d2e48e8 https://github.com/galaxyproject/galaxy/commit/212f7f4aabc6e859dfcbe00db2cf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: client/galaxy/scripts/mvc/library/library-dataset-view.js static/maps/mvc/library/library-dataset-view.js.map static/maps/mvc/library/library-folder-view.js.map static/maps/mvc/library/library-library-view.js.map static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/library/library-dataset-view.js static/scripts/mvc/library/library-folder-view.js static/scripts/mvc/library/library-library-view.js Compare: https://github.com/galaxyproject/galaxy/compare/00a55f8c0285...212f7f4aabc6

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[galaxyproject/galaxy] 92aff6: Fix for redirecting a non-user when a tool has req...
by GitHub 19 Apr '16

19 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 92aff618cb435f2b4d5805378e4bbcd67ae1f7a4 https://github.com/galaxyproject/galaxy/commit/92aff618cb435f2b4d5805378e4b… Author: Daniel Blankenberg <dan.blankenberg(a)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/e1d937e430a859997b252432cc1b… Author: Nicola Soranzo <nsoranzo(a)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/49a7328186bff37fc55725eb4b9a… Author: John Chilton <jmchilton(a)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/7d4030412d1aa58d0c3daa86d0ad…) Commit: cea9a12238b681892b8956dd6961383a9a025220 https://github.com/galaxyproject/galaxy/commit/cea9a12238b681892b8956dd6961… Author: guerler <aysam.guerler(a)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/ab015c67dff7261dfd233901fe6f… Author: Dannon Baker <dannon.baker(a)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/7ad55b7eb8ffb49d4cca299432a7… Author: Martin Cech <cech.marten(a)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/76386b5eab770b1f7fdb4afbf776… Author: Martin Cech <cech.marten(a)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/a85b5ee762009a95ff20273ece10… Author: Martin Cech <cech.marten(a)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/1fd326855d5b19b9b0fa7b078d26… Author: Martin Cech <cech.marten(a)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/53021ef33ea3e024d6a7b775fb1a… Author: John Chilton <jmchilton(a)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/9ea399694f2678fe99f14a9fdfd1… Author: carlfeberhard <carlfeberhard(a)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/5d39c84a71fdcf0611dd7e480c41… Author: carlfeberhard <carlfeberhard(a)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/980d37f50f324f097ca80b450826… Author: Martin Cech <cech.marten(a)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/35ab333c7e74275a1b31b49a8050… Author: Martin Cech <cech.marten(a)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/642fccd288415b36c2e8a1a72519… Author: Martin Cech <cech.marten(a)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/bbd76f139b3118f968f68cbc64c0… Author: guerler <aysam.guerler(a)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/db805184f5e4683c6529891b5c66… Author: Martin Cech <cech.marten(a)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/76691ab2e1474174670128ab81ba… Author: Martin Cech <cech.marten(a)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/75864e552b6a549c045e76a711fc… Author: Martin Cech <cech.marten(a)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/00a55f8c0285583727155d1b4d39… Author: John Chilton <jmchilton(a)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/78f35bfe84391554cfb3fbb05b50… Author: Nate Coraor <nate(a)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

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[galaxyproject/galaxy] 980d37: fix a bug with missing history_id in libraries dat...
by GitHub 19 Apr '16

19 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 980d37f50f324f097ca80b4508265c5160ac7ed0 https://github.com/galaxyproject/galaxy/commit/980d37f50f324f097ca80b450826… Author: Martin Cech <cech.marten(a)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/35ab333c7e74275a1b31b49a8050… Author: Martin Cech <cech.marten(a)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/642fccd288415b36c2e8a1a72519… Author: Martin Cech <cech.marten(a)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: 00a55f8c0285583727155d1b4d397a2b16a4af3c https://github.com/galaxyproject/galaxy/commit/00a55f8c0285583727155d1b4d39… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/75864e552b6a...00a55f8c0285

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[galaxyproject/galaxy] b95cca: always fetch new permissions as we are reusing the...
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: b95cca862cae9cf7e78370fd68ea5f530fb8194f https://github.com/galaxyproject/galaxy/commit/b95cca862cae9cf7e78370fd68ea… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- always fetch new permissions as we are reusing the view Commit: e2f88296f8454e9195ad1a6f2d4c9c9ade40ee77 https://github.com/galaxyproject/galaxy/commit/e2f88296f8454e9195ad1a6f2d4c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- Merge pull request #2176 from martenson/fix-permissions-caching [16.01] libraries: always fetch new permissions as we are reusing the view Compare: https://github.com/galaxyproject/galaxy/compare/9e278de39592...e2f88296f845

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