galaxy-commits April 2016

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[galaxyproject/galaxy] bbd76f: Fix message in legacy panel mako
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/76691ab2e147...75864e552b6a

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[galaxyproject/galaxy] 9ea399: UI, display_base: render links in header first
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/db805184f5e4...76691ab2e147

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[galaxyproject/galaxy] 49a732: More Pulsar fixes.
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy 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: 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. Compare: https://github.com/galaxyproject/galaxy/compare/53021ef33ea3...db805184f5e4

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[galaxyproject/galaxy] 7ad55b: try pushing again when we get unexpected exception...
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/ab015c67dff7...53021ef33ea3

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[galaxyproject/galaxy] f50504: Refactor checking tool files toward reuse with wor...
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f505041bdace98df66bff3851d1e03a7a349ddac https://github.com/galaxyproject/galaxy/commit/f505041bdace98df66bff3851d1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Refactor checking tool files toward reuse with workflow in planemo. Improve docstrings, import order, and interface definiton in that file as well. Updated with improved conditional pass through ``looks_like_a_cwl_artifact`` as spotted by @nsoranzo. Commit: f1c008b741cc08c4cf8dd982943dc4114f555e37 https://github.com/galaxyproject/galaxy/commit/f1c008b741cc08c4cf8dd982943d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #2183 from jmchilton/more_looks_like_tool Refactor checking tool files toward reuse with workflows in planemo. Compare: https://github.com/galaxyproject/galaxy/compare/d8e4f571aebc...f1c008b741cc

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[galaxyproject/galaxy] cea9a1: Replace masthead dom to avoid duplication
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/e1d937e430a8...ab015c67dff7

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[galaxyproject/galaxy] 92aff6: Fix for redirecting a non-user when a tool has req...
by GitHub 18 Apr '16

18 Apr '16

Branch: refs/heads/release_16.04 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. Compare: https://github.com/galaxyproject/galaxy/compare/1c38b9723cc2...e1d937e430a8

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[galaxyproject/infrastructure-playbook] 41ab2e: Changing node counts requires a full restart of at...
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 41ab2e608f38e19b7ace504bb7784ee042b358fc https://github.com/galaxyproject/infrastructure-playbook/commit/41ab2e608f3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M roles/slurm/handlers/main.yml M roles/slurm/tasks/main.yml Log Message: ----------- Changing node counts requires a full restart of at least slurmctld (not sure about slurmd)

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[galaxyproject/infrastructure-playbook] 1e5623: Fix Main deps
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1e56237a2890020820180aa32f14bed1a53b3285 https://github.com/galaxyproject/infrastructure-playbook/commit/1e56237a289… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/galaxynodes.yml Log Message: ----------- Fix Main deps

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[galaxyproject/infrastructure-playbook] c6135d: New TACC instances
by GitHub 15 Apr '16

15 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c6135dd5663dcc4c623495d5d77bfb174f7c2a03 https://github.com/galaxyproject/infrastructure-playbook/commit/c6135dd5663… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- New TACC instances

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galaxy-commits April 2016