Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: ff769585ecdf0f79b23cdf47829f003c4a1980d4
https://github.com/galaxyproject/usegalaxy-playbook/commit/ff769585ecdf0f79…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-05-26 (Thu, 26 May 2016)
Changed paths:
A production/host_vars/jetstream-iu0.galaxyproject.org.yml
M production/host_vars/jetstream-tacc0.galaxyproject.org.yml
M production/inventory
A stage/host_vars/jetstream-iu0.galaxyproject.org.yml
M stage/host_vars/jetstream-tacc0.galaxyproject.org.yml
M stage/inventory
Log Message:
-----------
Pulsar for Jetstream @ IU, also install Paste to fix Pulsar logging
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: be97d7e6db1d963c64dceeb06c68440500177ba5
https://github.com/galaxyproject/galaxy/commit/be97d7e6db1d963c64dceeb06c68…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/style/less/frame.less
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/ui/ui-frames.js
M static/style/blue/base.css
Log Message:
-----------
Replace frame dictionary with regular view
Commit: b9e2983e909cc74509214e864820467a256ea336
https://github.com/galaxyproject/galaxy/commit/b9e2983e909cc74509214e864820…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/style/less/frame.less
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/mvc/ui/ui-frames.js
Log Message:
-----------
Remove grid lock feature
Commit: 53fa566a54eb8d6be69e769ebd9799a9d392db3f
https://github.com/galaxyproject/galaxy/commit/53fa566a54eb8d6be69e769ebd97…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-frames.js
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-frames.js
M static/style/blue/base.css
Log Message:
-----------
Use regular initialization from frame shadow view
Commit: 44bd042624602648d87a24805e94e110102286ed
https://github.com/galaxyproject/galaxy/commit/44bd042624602648d87a24805e94…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/style/less/frame.less
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/ui/ui-frames.js
M static/style/blue/base.css
Log Message:
-----------
Add support for optional header items/icons
Commit: e16c3f34f39d0705a26081eafc5c321d6aca56c9
https://github.com/galaxyproject/galaxy/commit/e16c3f34f39d0705a26081eafc5c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-frames.js
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-frames.js
Log Message:
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Remove unused class variables, reduce indention
Commit: 64cb97cfc90fc93e550c1b74e1c62a9a0d4e656c
https://github.com/galaxyproject/galaxy/commit/64cb97cfc90fc93e550c1b74e1c6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/ui/ui-frames.js
Log Message:
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Parse view instead of content dom on click
Commit: 617cd2de82caca3f174479d3602bb45236da5175
https://github.com/galaxyproject/galaxy/commit/617cd2de82caca3f174479d3602b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/style/less/frame.less
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/ui/ui-frames.js
M static/style/blue/base.css
Log Message:
-----------
Add event handlers to navigate through history
Commit: a12c1cb45ba3026c2ff6d8cc9d70c622e26718f6
https://github.com/galaxyproject/galaxy/commit/a12c1cb45ba3026c2ff6d8cc9d70…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
Log Message:
-----------
Cache histories individually
Commit: 197f2283f92ed851c8a8254eb6c020b90023188d
https://github.com/galaxyproject/galaxy/commit/197f2283f92ed851c8a8254eb6c0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/history-model.js
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/histories.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
A lib/galaxy/tools/verify/__init__.py
A lib/galaxy/tools/verify/asserts/__init__.py
A lib/galaxy/tools/verify/asserts/tabular.py
A lib/galaxy/tools/verify/asserts/text.py
A lib/galaxy/tools/verify/asserts/xml.py
A lib/galaxy/tools/verify/test_data.py
M static/maps/mvc/history/history-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/history/history-model.js
M templates/show_params.mako
M test/api/test_tools.py
M test/api/test_workflows.py
R test/base/asserts/__init__.py
R test/base/asserts/tabular.py
R test/base/asserts/text.py
R test/base/asserts/xml.py
R test/base/test_data.py
M test/base/twilltestcase.py
M test/functional/test_toolbox.py
A test/functional/tools/composite_output_tests.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/simple_constructs.yml
M test/shed_functional/base/twilltestcase.py
M test/unit/managers/test_HistoryManager.py
M tools/stats/gsummary.xml
Log Message:
-----------
Merge branch 'dev' into scratchbook_slider_000
Commit: 27b70ca9849b241c93958c4b18af38ec576cbd3e
https://github.com/galaxyproject/galaxy/commit/27b70ca9849b241c93958c4b18af…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-05-26 (Thu, 26 May 2016)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/style/less/frame.less
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/ui/ui-frames.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #2396 from guerler/scratchbook_slider_000
Add history navigation options for dataset frames to scratch book
Compare: https://github.com/galaxyproject/galaxy/compare/50359e1633b5...27b70ca9849b
Branch: refs/heads/master
Home: https://github.com/galaxyproject/galaxy
Commit: 66947c20ef2c0db3532d7e4f3edc5897d7d75ab7
https://github.com/galaxyproject/galaxy/commit/66947c20ef2c0db3532d7e4f3edc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-05-23 (Mon, 23 May 2016)
Changed paths:
A lib/galaxy/datatypes/checkers.py
M lib/galaxy/util/checkers.py
Log Message:
-----------
Provide backward-compatible galaxy.datatypes.checkers module.
xref http://dev.list.galaxyproject.org/STACKS-error-td4669428.html
Commit: 5fbb65e5033d23b9751251a4a935b4c76ffd65d5
https://github.com/galaxyproject/galaxy/commit/5fbb65e5033d23b9751251a4a935…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-05-24 (Tue, 24 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/slurm.py
Log Message:
-----------
Catch all exceptions in slurm's _complete_terminal_job() to prevent
looping job completion
Commit: b6d65da83d77167482a3fe3a706c249abad6dbfa
https://github.com/galaxyproject/galaxy/commit/b6d65da83d77167482a3fe3a706c…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-05-24 (Tue, 24 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/slurm.py
Log Message:
-----------
Fix linting error
Commit: 2a29e92ef9d8e560988d6e64d06c5cbbf79098a1
https://github.com/galaxyproject/galaxy/commit/2a29e92ef9d8e560988d6e64d06c…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-05-24 (Tue, 24 May 2016)
Changed paths:
M lib/galaxy/managers/histories.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
API, history: fix order in most_recently_used
- Fix ascending order used in HistoryManager.most_recent to descending
- Slightly update the docs to reflect actual value better
- Add tests
Commit: 47a65160960003244091d4fd441111c257e9e8d9
https://github.com/galaxyproject/galaxy/commit/47a65160960003244091d4fd4411…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M lib/galaxy/managers/histories.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Merge pull request #2407 from carlfeberhard/fix.most_recently_used
[16.01] API, history: fix order in most_recently_used
Commit: 7dcf850ed5203196371fa3d20800b0b864c01158
https://github.com/galaxyproject/galaxy/commit/7dcf850ed5203196371fa3d20800…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/slurm.py
Log Message:
-----------
Merge pull request #2402 from natefoo/slurm-fixes
[16.04] Catch all exceptions in slurm's _complete_terminal_job() to prevent looping job completion
Commit: 5db5e1395880876ac3066fc91397e7cb1618ea62
https://github.com/galaxyproject/galaxy/commit/5db5e1395880876ac3066fc91397…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M lib/galaxy/managers/histories.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Merge branch 'release_16.01' into release_16.04
Conflicts:
test/unit/managers/test_HistoryManager.py
Commit: 71f9d9621640ca77880a879da3a149467f5ec934
https://github.com/galaxyproject/galaxy/commit/71f9d9621640ca77880a879da3a1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/util/checkers.py
Log Message:
-----------
Remove HTML_CHECK_LINES from checkers export.
As suggested by @nsoranzo and @dannon, we will restore if and only if someone finds a datatype that uses it.
Commit: c63bf911bc9cae4d0400a3f3fad03402c3f7a18a
https://github.com/galaxyproject/galaxy/commit/c63bf911bc9cae4d0400a3f3fad0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
A lib/galaxy/datatypes/checkers.py
M lib/galaxy/util/checkers.py
Log Message:
-----------
Merge pull request #2389 from jmchilton/checkers_restore
[16.04] Provide backward compatible galaxy.datatypes.checkers module...
Commit: 5a97b8feac49df3f1e9fe0b2e0645b9240eb8291
https://github.com/galaxyproject/galaxy/commit/5a97b8feac49df3f1e9fe0b2e064…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
A lib/galaxy/datatypes/checkers.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/histories.py
M lib/galaxy/util/checkers.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Merge branch 'release_16.04'
Compare: https://github.com/galaxyproject/galaxy/compare/ac5a328e5f56...5a97b8feac49
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: c5c03b561aa331a1029a5b4d7775370c4d4b941a
https://github.com/galaxyproject/infrastructure-playbook/commit/c5c03b561aa…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M jetstreamiuenv/group_vars/controllers.yml
M jetstreamiuenv/playbook.yml
A jetstreamiuenv/templates/supervisor/pulsar.j2
M jetstreamtaccenv/group_vars/controllers.yml
A jetstreamtaccenv/templates/supervisor/pulsar.j2
Log Message:
-----------
Run Pulsar with supervisor on Jetstream
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2e45e77fa82b723ebb5dc6c398891c3a061c6961
https://github.com/galaxyproject/galaxy/commit/2e45e77fa82b723ebb5dc6c39889…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/history-model.js
M static/maps/mvc/history/history-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/history/history-model.js
Log Message:
-----------
UI, history: correctly handle index API defaults
Bypasses the histories.index default `deleted=False` flag when using
HistoryCollection to fetch with `includeDeleted`.
Commit: f0a1bc8cbdfa796e5293b66dbcc846ad6f624aa1
https://github.com/galaxyproject/galaxy/commit/f0a1bc8cbdfa796e5293b66dbcc8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/history-model.js
M static/maps/mvc/history/history-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/history/history-model.js
Log Message:
-----------
Merge pull request #2413 from carlfeberhard/fix.history-collection
UI, history: correctly handle index API defaults
Compare: https://github.com/galaxyproject/galaxy/compare/81702e7fbaec...f0a1bc8cbdfa