Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 52a5f6e2dbf24202258973c706e08f15d1d5a44b
https://github.com/galaxyproject/galaxy/commit/52a5f6e2dbf24202258973c706e0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-06-01 (Wed, 01 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Properly display subworkflows in new run workflow form
Commit: dcd07221a8a00250dc8dc171ab480d8ba7f3b323
https://github.com/galaxyproject/galaxy/commit/dcd07221a8a00250dc8dc171ab48…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-06-01 (Wed, 01 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Remove output details from success message
Commit: 7eaf40ec56ed186289972883410b059ded993e7b
https://github.com/galaxyproject/galaxy/commit/7eaf40ec56ed186289972883410b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-06-01 (Wed, 01 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Re-add new history links to success message
Commit: 1b3eaeb299bb29460c1ebd24c881d2921631987b
https://github.com/galaxyproject/galaxy/commit/1b3eaeb299bb29460c1ebd24c881…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-06-02 (Thu, 02 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-select-content.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/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Fix batchmode labels
Commit: a0dbcb93a3cb1e3a108b07272946e9fe36e0b376
https://github.com/galaxyproject/galaxy/commit/a0dbcb93a3cb1e3a108b07272946…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-06-02 (Thu, 02 Jun 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-select-content.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/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-select-content.js
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Merge pull request #2440 from guerler/fix_subworkflows_display
Properly list subworkflows in run workflow form
Compare: https://github.com/galaxyproject/galaxy/compare/84ece6da372e...a0dbcb93a3cb
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a27e86786ad031eafcbfeb39ffdadf71d80dcfad
https://github.com/galaxyproject/galaxy/commit/a27e86786ad031eafcbfeb39ffda…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-05-26 (Thu, 26 May 2016)
Changed paths:
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/repository_types/metadata.py
M tools/filters/axt_to_lav.py
Log Message:
-----------
wrap bare str raises with generic Exception()
as Pyton 2.7 does not support bare str
Commit: fe64a8198bca75f2e535efc7c3813d24810904ab
https://github.com/galaxyproject/galaxy/commit/fe64a8198bca75f2e535efc7c381…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-05-26 (Thu, 26 May 2016)
Changed paths:
M lib/galaxy/security/__init__.py
Log Message:
-----------
fix the mess made with mass edit
Commit: 6094990e43f6510833395885d234a2264e7d44f1
https://github.com/galaxyproject/galaxy/commit/6094990e43f6510833395885d234…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-05-26 (Thu, 26 May 2016)
Changed paths:
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/repository_types/metadata.py
M tools/filters/axt_to_lav.py
Log Message:
-----------
Merge pull request #2424 from martenson/port-exceptionwrap-16.04
[16.04] wrap bare str exceptions
Commit: 214e757d81623e9c12d171f3dcfc516c7dcc5e32
https://github.com/galaxyproject/galaxy/commit/214e757d81623e9c12d171f3dcfc…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-05-31 (Tue, 31 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/slurm.py
Log Message:
-----------
Only scan the last 16 MB of a job's stderr for slurm memory warning
messages.
Commit: dcb28e095012fef3be769f677fa572f13d4ed88a
https://github.com/galaxyproject/galaxy/commit/dcb28e095012fef3be769f677fa5…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-05-31 (Tue, 31 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/slurm.py
Log Message:
-----------
Fix linting error
Commit: ceb825bea8b28c8908c8a719919b9167bedabe55
https://github.com/galaxyproject/galaxy/commit/ceb825bea8b28c8908c8a719919b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-05-31 (Tue, 31 May 2016)
Changed paths:
M lib/galaxy/jobs/runners/slurm.py
Log Message:
-----------
Merge pull request #2432 from natefoo/job-output-memory-fix
[16.04] Only scan the last 16 MB of a job's stderr for slurm memory warning messages
Commit: 7cb527ac595591c99401436757168b366f86a526
https://github.com/galaxyproject/galaxy/commit/7cb527ac595591c9940143675716…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-06-02 (Thu, 02 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/slurm.py
Log Message:
-----------
Overwrite the correct part of stderr
- Skip partial line
- Seek back to the correct position after readlines()
- Use the same approach in __check_memory_limit()
Commit: 58f3f5c7dd4c622adce0f18d24a0ee950d1d4dfd
https://github.com/galaxyproject/galaxy/commit/58f3f5c7dd4c622adce0f18d24a0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-06-02 (Thu, 02 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/slurm.py
Log Message:
-----------
Merge pull request #2447 from nsoranzo/release_16.04_fix_for_2432
[16.04] Overwrite the correct part of stderr
Commit: 84ece6da372ea0e0537bf68c6981962437e0d330
https://github.com/galaxyproject/galaxy/commit/84ece6da372ea0e0537bf68c6981…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-06-02 (Thu, 02 Jun 2016)
Changed paths:
M lib/galaxy/jobs/runners/slurm.py
Log Message:
-----------
Merge branch 'release_16.04' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/ec476c7cb46a...84ece6da372e
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: fd36eee5572fe6871216411fe85dc892ae8e3b6e
https://github.com/galaxyproject/infrastructure-playbook/commit/fd36eee5572…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-06-02 (Thu, 02 Jun 2016)
Changed paths:
M galaxyenv/host_vars/cvmfs0-tacc0.galaxyproject.org.yml
M roles/cvmfs/defaults/main.yml
M roles/cvmfs/tasks/stratum0.yml
M roles/cvmfs/tasks/stratum1.yml
A taccenv/host_vars/galaxy04.tacc.utexas.edu.yml
M taccenv/inventory
M taccenv/playbook.yml
A taccenv/secret_group_vars/baseenv.yml
A taccenv/secret_group_vars/galaxymainservers.yml
A taccenv/secret_group_vars/galaxytestservers.yml
A taccenv/secret_host_vars/default.yml
A taccenv/secret_host_vars/galaxy04.tacc.utexas.edu.yml
Log Message:
-----------
Allow Galaxy Team members to log in to cvmfs0-tacc0 to update Test and Main.
Stratum1 and client permissions coming soon.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d458906f37239be23552cf9df86dfa066270e54c
https://github.com/galaxyproject/galaxy/commit/d458906f37239be23552cf9df86d…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-06-02 (Thu, 02 Jun 2016)
Changed paths:
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Raven: fix import in galaxy.panels.mako
Raven now uses a UMD and checks for requirejs removing it from globals
if found. This adds a require import to load Raven.
Commit: 8ef5279aacc6125908a37a9157feb47c7c556104
https://github.com/galaxyproject/galaxy/commit/8ef5279aacc6125908a37a9157fe…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-06-02 (Thu, 02 Jun 2016)
Changed paths:
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Raven: revert previous commit and move raven first
Moves galaxy.panels.mako's import of Raven back to vanilla script
tag and before the requirejs library import, allowing Raven's UMD
to define Raven as a global.
This starts Raven/sentry *before* the library package is loaded so that
library errors can be captured as well.
Commit: f78d5404a27d13e0a4e14e655673357d1497f7b2
https://github.com/galaxyproject/galaxy/commit/f78d5404a27d13e0a4e14e655673…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-06-02 (Thu, 02 Jun 2016)
Changed paths:
M client/bower.json
R client/galaxy/scripts/libs/tracekit.js
M client/grunt-tasks/install-libs.js
R static/maps/libs/tracekit.js.map
R static/scripts/libs/tracekit.js
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
Log Message:
-----------
Raven: remove tracekit as raven has its own
Commit: ec476c7cb46a89ae222a65ff8fe0bb468d989bfd
https://github.com/galaxyproject/galaxy/commit/ec476c7cb46a89ae222a65ff8fe0…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-06-02 (Thu, 02 Jun 2016)
Changed paths:
M client/bower.json
R client/galaxy/scripts/libs/tracekit.js
M client/grunt-tasks/install-libs.js
R static/maps/libs/tracekit.js.map
R static/scripts/libs/tracekit.js
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Merge pull request #2445 from carlfeberhard/fix.raven
Fix raven.js import order in galaxy.panels.mako
Compare: https://github.com/galaxyproject/galaxy/compare/25a26d8c9c4f...ec476c7cb46a