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July 2016
- 1 participants
- 109 discussions
26 Jul '16
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: 4a831033ed820e3f1220d9d326f8bd8079c390f9
https://github.com/galaxyproject/galaxy/commit/4a831033ed820e3f1220d9d326f8…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Generate metadata in separate conda environment
Galaxy supports generating metadata in a separate command (enable
beta_tool_command_isolation). This command has its own dependency resolution,
that may interfere with thedependency resolution of the actual tool, if the
same environment is being used. With this PR we create a new environment when
resolving metadata dependencies with conda, that will be active only for
metadata generation.
Commit: 28da4b6371b23c69d15e7fc59473d4bde5639fde
https://github.com/galaxyproject/galaxy/commit/28da4b6371b23c69d15e7fc59473…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Fix whitespace and comma use
Commit: f8cf81d73693e5f075b6c9e612244221bbd6e5bb
https://github.com/galaxyproject/galaxy/commit/f8cf81d73693e5f075b6c9e61224…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
Log Message:
-----------
Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore.
Commit: f0024d64e15815dcb6c2ac027ed5fb2977651e64
https://github.com/galaxyproject/galaxy/commit/f0024d64e15815dcb6c2ac027ed5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/web/framework/helpers/__init__.py
M test/base/driver_util.py
Log Message:
-----------
Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it)
Commit: 8f978b8957f0cbc7e5d78ca3f3bce9e87e6e8f76
https://github.com/galaxyproject/galaxy/commit/8f978b8957f0cbc7e5d78ca3f3bc…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/web/framework/helpers/__init__.py
M test/base/driver_util.py
Log Message:
-----------
Merge pull request #2662 from jmchilton/backport_2253
[16.04] Backport #2253 as requested by Eagle Eyes
Compare: https://github.com/galaxyproject/galaxy/compare/1de7beca98d0...8f978b8957f0
1
0
[galaxyproject/galaxy] c07bbe: Add import order linting using tox and flake8-impo...
by GitHub 26 Jul '16
by GitHub 26 Jul '16
26 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c07bbe010ee350d6bb63006ff8829a16d0d9d4a9
https://github.com/galaxyproject/galaxy/commit/c07bbe010ee350d6bb63006ff882…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
A .ci/flake8_lint_include_list.txt
A .ci/flake8_wrapper_imports.sh
M .travis.yml
M setup.cfg
M tox.ini
Log Message:
-----------
Add import order linting using tox and flake8-import-order.
Adds two tasks:
- Add a task that just lints everything the way Galaxy's default linting is (py27-lint-imports) and don't enforce it passes on Travis.
- Add a task that just lints a subset we expect to past, hopefully we can grow this subset over time.
Once the inverse of the subset we are testing is just the blacklist, we can eliminate bothtasks and just wrap this into Galaxy's default linting.
These tasks require an older flake8 until https://github.com/PyCQA/flake8-import-order/issues/79#issuecomment-2350522… is part of a released version of flake8.
Commit: 8b597ed01a6fd4335b78ba66875a40f430423c34
https://github.com/galaxyproject/galaxy/commit/8b597ed01a6fd4335b78ba66875a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
A .ci/flake8_lint_include_list.txt
A .ci/flake8_wrapper_imports.sh
M .travis.yml
M setup.cfg
M tox.ini
Log Message:
-----------
Merge pull request #2661 from jmchilton/lint_imports
Add import order linting using tox and flake8-import-order.
Compare: https://github.com/galaxyproject/galaxy/compare/71151c6b2dd3...8b597ed01a6f
1
0
[galaxyproject/galaxy] 26b141: made changes to tool-form-base.js, this should all...
by GitHub 26 Jul '16
by GitHub 26 Jul '16
26 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 26b141c83f906dbc7d11c14da968f323eaa632e8
https://github.com/galaxyproject/galaxy/commit/26b141c83f906dbc7d11c14da968…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
made changes to tool-form-base.js, this should allow the tool-form to listen to history. Thanks @guerler for walking me through backbone
Commit: c172641c9deda5d9c193e212a2d74d150eb64f79
https://github.com/galaxyproject/galaxy/commit/c172641c9deda5d9c193e212a2d7…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.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-base.js
Log Message:
-----------
added refresh in _buildform as per @guerler 's suggestion
Commit: fd34553cb142e9ccff6b7b295247dd09801d3fb0
https://github.com/galaxyproject/galaxy/commit/fd34553cb142e9ccff6b7b295247…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.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-base.js
Log Message:
-----------
removing options.needs_update as it is not used anymore, per @guerlers suggestion
Commit: 6414478ad1ab669c8725d0fb784e1b438ddb40dd
https://github.com/galaxyproject/galaxy/commit/6414478ad1ab669c8725d0fb784e…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.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-base.js
Log Message:
-----------
added self.deferred() in refresh
Commit: a6e288fe301c00e88893e0ffe3cbe9f9572aba5e
https://github.com/galaxyproject/galaxy/commit/a6e288fe301c00e88893e0ffe3cb…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
changes'
Commit: 71151c6b2dd3038ac04a77bbb8543e77875b9cc1
https://github.com/galaxyproject/galaxy/commit/71151c6b2dd3038ac04a77bbb854…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Merge pull request #2476 from nturaga/tool_form_listen_history
Allow tool form to listen to history
Compare: https://github.com/galaxyproject/galaxy/compare/3d0f5577b105...71151c6b2dd3
1
0
[galaxyproject/galaxy] 7a8d86: Ensure Galaxy's python binary is used for metadata...
by GitHub 26 Jul '16
by GitHub 26 Jul '16
26 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7a8d86aa9bd2b8adfbe8e6826e506dfedf997e22
https://github.com/galaxyproject/galaxy/commit/7a8d86aa9bd2b8adfbe8e6826e50…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Ensure Galaxy's python binary is used for metadata generation.
Commit: 3d0f5577b10507cd774f3e4f92f6c8364a8a4407
https://github.com/galaxyproject/galaxy/commit/3d0f5577b10507cd774f3e4f92f6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Merge pull request #2660 from jmchilton/ensure_galaxy_python_for_metadata
Ensure Galaxy's python binary is used for metadata generation.
Compare: https://github.com/galaxyproject/galaxy/compare/9607e528be01...3d0f5577b105
1
0
[galaxyproject/galaxy] 93ba35: Import pyparsing in testing so twill's older versi...
by GitHub 26 Jul '16
by GitHub 26 Jul '16
26 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 93ba35fdd16a96b46ccac6884b7efcb4a5d3e8a3
https://github.com/galaxyproject/galaxy/commit/93ba35fdd16a96b46ccac6884b7e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M test/base/twilltestcase.py
Log Message:
-----------
Import pyparsing in testing so twill's older version doesn't get loaded.
There are unintended consequences if not, such as svgwrite not loading properly.
Commit: 9607e528be01234b1107db29e0a910043d12507e
https://github.com/galaxyproject/galaxy/commit/9607e528be01234b1107db29e0a9…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-26 (Tue, 26 Jul 2016)
Changed paths:
M test/base/twilltestcase.py
Log Message:
-----------
Merge pull request #2656 from jmchilton/pyparsing_testing
Import pyparsing in testing so twill's older version doesn't get loaded.
Compare: https://github.com/galaxyproject/galaxy/compare/134f98854931...9607e528be01
1
0
[galaxyproject/galaxy] 8559dc: Ignore .tox directory. Used to be ignored by defa...
by GitHub 25 Jul '16
by GitHub 25 Jul '16
25 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8559dc00b606551de5947d6bc5d74bb9feb9f184
https://github.com/galaxyproject/galaxy/commit/8559dc00b606551de5947d6bc5d7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
Log Message:
-----------
Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore.
Commit: 10745f252f6e0cf59a47f097620d5d05034b1c1a
https://github.com/galaxyproject/galaxy/commit/10745f252f6e0cf59a47f097620d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M lib/galaxy/web/framework/helpers/__init__.py
M test/base/driver_util.py
Log Message:
-----------
Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it)
Commit: cf800dce03949e928333a13b675fba76e612226f
https://github.com/galaxyproject/galaxy/commit/cf800dce03949e928333a13b675f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
Log Message:
-----------
Add eggs to blacklist as well, to ignore it in local testing for folks with it still around. (nsoranzo's suggestion)
Commit: 9f2237905b81205d0d6fec918fc15ddbea1e34ce
https://github.com/galaxyproject/galaxy/commit/9f2237905b81205d0d6fec918fc1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M lib/galaxy/model/mapping.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M test/base/driver_util.py
Log Message:
-----------
Remove two #noqas and specify __all__ for those modules. Specify many more #noqas to skip the precise relevant exception.
Commit: 0deae302852102c66e6386e16607c1db99cdeb07
https://github.com/galaxyproject/galaxy/commit/0deae302852102c66e6386e16607…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/forms.py
Log Message:
-----------
Remove two unused imports in forms controller.
Commit: 134f988549314a4a384144c2eedc3d8b4ff7e2f3
https://github.com/galaxyproject/galaxy/commit/134f988549314a4a384144c2eedc…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/galaxy/model/mapping.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M test/base/driver_util.py
Log Message:
-----------
Merge pull request #2650 from dannon/flake8_update_tox_default
Ignore .tox directory. Used to be ignored by default w/ flake8 appar…
Compare: https://github.com/galaxyproject/galaxy/compare/1e291e1ecdd1...134f98854931
1
0
25 Jul '16
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 796678f38f5545c1efc9eb1b2ba1ffa8d1244019
https://github.com/galaxyproject/usegalaxy-playbook/commit/796678f38f5545c1…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M common_roles
M production/galaxy_version.yml
Log Message:
-----------
update Main, update submodule
1
0
25 Jul '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0dd206d8f6851eeeb4fa513c42f053f801c6b757
https://github.com/galaxyproject/galaxy/commit/0dd206d8f6851eeeb4fa513c42f0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-buttons.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-buttons.js
M static/style/blue/base.css
Log Message:
-----------
Add optional progress bar to default buttons
Commit: d5a16deb00dc68176c04c8ed1ab1005e346f057c
https://github.com/galaxyproject/galaxy/commit/d5a16deb00dc68176c04c8ed1ab1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Increase bar size, modify wait label
Commit: bc6358ea35e6904cd7a9264fcb32ab5f8e0aa5d3
https://github.com/galaxyproject/galaxy/commit/bc6358ea35e6904cd7a9264fcb32…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M static/style/blue/base.css
Log Message:
-----------
Repack styles
Commit: 7ef6a99959511d600e64c01453b68fc4677323d7
https://github.com/galaxyproject/galaxy/commit/7ef6a99959511d600e64c01453b6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 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:
-----------
Disable button before validation
Commit: ceaa5991e08e3e2b0a036f4b59d148b5608ec1ad
https://github.com/galaxyproject/galaxy/commit/ceaa5991e08e3e2b0a036f4b59d1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M config/datatypes_conf.xml.sample
A display_applications/ucsc/trackhub.xml
A lib/galaxy/datatypes/hubAssembly.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/tools/execute.py
M lib/galaxy/workflow/extract.py
Log Message:
-----------
Merge branch 'dev' into progress_button
Commit: be7210e03bc6867baba513d3fb879e00bce169b4
https://github.com/galaxyproject/galaxy/commit/be7210e03bc6867baba513d3fb87…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M static/style/blue/base.css
Log Message:
-----------
Place steps into scrollable div, restyle step forms
Fix
Commit: 5120637b00c8c3ecef5e2caf95b7be32c4bac86d
https://github.com/galaxyproject/galaxy/commit/5120637b00c8c3ecef5e2caf95b7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.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-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/style/blue/base.css
Log Message:
-----------
Remove operations from workflow step modules to simplify view
Commit: d0e222f529755e060edd3837d4fc57754c6b0447
https://github.com/galaxyproject/galaxy/commit/d0e222f529755e060edd3837d4fc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M static/maps/mvc/form/form-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/form/form-view.js
Log Message:
-----------
Generalize input element highlighting
Commit: 95949c66bc658afc285dae854efd2fa8c8ede6e0
https://github.com/galaxyproject/galaxy/commit/95949c66bc658afc285dae854efd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
M .ci/py3_sources.txt
M .gitignore
A client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/style/less/base.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M lib/galaxy/config.py
R lib/galaxy/datatypes/hubAssembly.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/users.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A scripts/communication/communication_server.py
A scripts/communication/template/communication.css
A scripts/communication/template/communication.html
A scripts/communication/template/communication.js
A static/maps/layout/generic-nav-view.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/layout/generic-nav-view.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
A static/style/base.css
M static/style/blue/base.css
A templates/user/communication_settings.mako
M templates/user/index.mako
Log Message:
-----------
Merge branch 'dev' into progress_button
Commit: 8cf69f382a4e81bd0c1e2eced57fdf67acc29a69
https://github.com/galaxyproject/galaxy/commit/8cf69f382a4e81bd0c1e2eced57f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-07-24 (Sun, 24 Jul 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 unused history div, use reduce to calculate available screen space
Commit: 1e291e1ecdd17344aad4baed295f00bc827e36f7
https://github.com/galaxyproject/galaxy/commit/1e291e1ecdd17344aad4baed295f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-buttons.js
M static/style/blue/base.css
Log Message:
-----------
Merge pull request #2647 from guerler/progress_button
Enhance workflow run button to indicate workflow loading progress, keep header fixed
Compare: https://github.com/galaxyproject/galaxy/compare/1b1e2876f562...1e291e1ecdd1
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 36938e8bcb5bba81dbac8df2a0314a96a881d50a
https://github.com/galaxyproject/galaxy/commit/36938e8bcb5bba81dbac8df2a031…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
Log Message:
-----------
Reorder base templates meta tags
Move title below recommended first three meta tags:
https://github.com/joshbuchea/HEAD#recommended-minimum
Commit: 1b1e2876f562c39227a2834d1c8d47d4f2a064e3
https://github.com/galaxyproject/galaxy/commit/1b1e2876f562c39227a2834d1c8d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-07-25 (Mon, 25 Jul 2016)
Changed paths:
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
Log Message:
-----------
Merge pull request #2651 from carlfeberhard/templates.meta-reorder
Reorder base templates meta tags
Compare: https://github.com/galaxyproject/galaxy/compare/5e4986875d8c...1b1e2876f562
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ef58e62e6deeeecd37587c737b3113ede606f3c1
https://github.com/galaxyproject/galaxy/commit/ef58e62e6deeeecd37587c737b31…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-05-05 (Thu, 05 May 2016)
Changed paths:
M .gitignore
Log Message:
-----------
excluded IntelliJ IDEA files
Commit: f1a3086b87536a78c757b25d5dab51a82ee8259b
https://github.com/galaxyproject/galaxy/commit/f1a3086b87536a78c757b25d5dab…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-24 (Tue, 24 May 2016)
Changed paths:
M .ci/flake8_wrapper.sh
M .ci/py3_sources.txt
M .gitignore
M CONTRIBUTORS.md
M Makefile
M README.rst
R buildbot_setup.sh
M client/README.md
M client/bower.json
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/libs/backbone.js
M client/galaxy/scripts/libs/bootstrap-tour.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/jquery/jquery.migrate.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
M client/galaxy/scripts/libs/underscore.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
R client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.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-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
R client/galaxy/scripts/mvc/tool/tool-template.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
A client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-select.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/metrics-logger.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/ui.less
M client/grunt-tasks/scripts.js
M client/grunt-tasks/style.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.scratchbook.yaml
M config/plugins/visualizations/charts/static/views/group.js
R config/plugins/visualizations/graphview/config/graphview.xml
R config/plugins/visualizations/graphview/static/graphview.css
R config/plugins/visualizations/graphview/static/graphview.js
R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js
R config/plugins/visualizations/graphview/templates/graphview.mako
M config/reports.ini.sample
M config/tool_data_table_conf.xml.sample
M config/tool_shed.ini.sample
M contrib/galaxy.debian-init
A contrib/galaxy_supervisor.conf
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
A display_applications/biom/biom_simple.xml
M doc/source/lib/modules.rst
R doc/source/lib/pulsar.client.rst
R doc/source/lib/pulsar.client.staging.rst
R doc/source/lib/pulsar.client.transport.rst
R doc/source/lib/pulsar.rst
M doc/source/releases/16.01.rst
A doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
A doc/source/releases/16.07_announce.rst
M doc/source/releases/index.rst
R install_and_test_tool_shed_repositories.sh
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
A lib/galaxy/datatypes/molecules.py
A lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/5e5z.pdb
A lib/galaxy/datatypes/test/drugbank_drugs.cml
A lib/galaxy/datatypes/test/drugbank_drugs.inchi
A lib/galaxy/datatypes/test/drugbank_drugs.mol2
A lib/galaxy/datatypes/test/drugbank_drugs.sdf
A lib/galaxy/datatypes/test/drugbank_drugs.smi
A lib/galaxy/datatypes/test/issue1818.tabular
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
A lib/galaxy/datatypes/test/q.fps
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/model/util.py
M lib/galaxy/openid/providers.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
A lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/__init__.py
M lib/galaxy/tools/linters/citations.py
M lib/galaxy/tools/linters/command.py
A lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
R lib/galaxy/tools/linters/top_level.py
M lib/galaxy/tools/linters/xml_order.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
R lib/galaxy/util/backports/importlib/__init__.py
R lib/galaxy/util/dictobj.py
M lib/galaxy/util/directory_hash.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/jstree.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/validation.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/biostar.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/vcf.py
R lib/pulsar/__init__.py
R lib/pulsar/client/__init__.py
R lib/pulsar/client/action_mapper.py
R lib/pulsar/client/amqp_exchange.py
R lib/pulsar/client/amqp_exchange_factory.py
R lib/pulsar/client/client.py
R lib/pulsar/client/config_util.py
R lib/pulsar/client/decorators.py
R lib/pulsar/client/destination.py
R lib/pulsar/client/interface.py
R lib/pulsar/client/job_directory.py
R lib/pulsar/client/manager.py
R lib/pulsar/client/object_client.py
R lib/pulsar/client/path_mapper.py
R lib/pulsar/client/setup_handler.py
R lib/pulsar/client/staging/__init__.py
R lib/pulsar/client/staging/down.py
R lib/pulsar/client/staging/up.py
R lib/pulsar/client/transport/__init__.py
R lib/pulsar/client/transport/curl.py
R lib/pulsar/client/transport/poster.py
R lib/pulsar/client/transport/requests.py
R lib/pulsar/client/transport/ssh.py
R lib/pulsar/client/transport/standard.py
R lib/pulsar/client/util.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.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/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/galaxy_install/utility_containers/__init__.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
R lib/tool_shed/scripts/api/add_repository_registry_entry.py
R lib/tool_shed/scripts/api/common.py
R lib/tool_shed/scripts/api/create_categories.py
R lib/tool_shed/scripts/api/create_users.py
R lib/tool_shed/scripts/api/export.py
R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py
R lib/tool_shed/scripts/api/import_capsule.py
R lib/tool_shed/scripts/api/remove_repository_registry_entry.py
R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh
R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py
R lib/tool_shed/scripts/check_repositories_for_functional_tests.py
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R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
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M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
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M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/xml_util.py
M lib/tool_shed/utility_containers/__init__.py
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A scripts/api/filter_failed_datasets_from_collection.py
M scripts/api/search.py
M scripts/api/upload_to_history.py
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M scripts/check_galaxy.py
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M scripts/cleanup_datasets/pgcleanup.py
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M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
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M scripts/cleanup_datasets/update_dataset_size.py
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M scripts/data_libraries/build_whoosh_index.py
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M scripts/drmaa_external_runner.py
M scripts/extract_dataset_part.py
M scripts/functional_tests.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
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M scripts/summarize_timings.py
A scripts/tool_shed/api/add_repository_registry_entry.py
A scripts/tool_shed/api/common.py
A scripts/tool_shed/api/create_categories.py
A scripts/tool_shed/api/create_users.py
A scripts/tool_shed/api/export.py
A scripts/tool_shed/api/get_filtered_repository_revisions.py
A scripts/tool_shed/api/import_capsule.py
A scripts/tool_shed/api/remove_repository_registry_entry.py
A scripts/tool_shed/api/reset_metadata_on_repositories.py
A scripts/tool_shed/api/tool_shed_repository_revision_update.py
A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh
A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh
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M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
A test/unit/shed_unit/__init__.py
A test/unit/shed_unit/test_fabric_util.py
A test/unit/shed_unit/test_td_common_util.py
A test/unit/shed_unit/test_tool_panel_manager.py
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M test/unit/test_objectstore.py
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M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
A tool-data/biom_simple_display.loc.sample
M tools/data_source/biomart.xml
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M tools/data_source/fetch.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_concat_fasta.xml
M tools/filters/axt_to_fasta.xml
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav.xml
M tools/filters/bed2gff.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/bed_to_gff_converter.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff2bed.xml
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M tools/filters/gtf2bedgraph.xml
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M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/trimmer.xml
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/filtering.xml
M tools/stats/grouping.py
M tools/stats/grouping.xml
M tools/stats/gsummary.py
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
Commit: d2c53ee724041ed6947b6db35665fd9ebb624ca8
https://github.com/galaxyproject/galaxy/commit/d2c53ee724041ed6947b6db35665…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-24 (Tue, 24 May 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
add config objects for the communication server
Commit: 20f25f0e35a8ca8b979aa971626925e413e39130
https://github.com/galaxyproject/galaxy/commit/20f25f0e35a8ca8b979aa9716269…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M lib/galaxy/managers/configuration.py
Log Message:
-----------
add communication host/port to the URL
Commit: f8a20cb85fa072bc2539a59c1869599be0137bfd
https://github.com/galaxyproject/galaxy/commit/f8a20cb85fa072bc2539a59c1869…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
A scripts/communication_server.py
Log Message:
-----------
add rt-communication server based on flask
Commit: e9642720b81b8ef9aed083b49fb2bc191333b376
https://github.com/galaxyproject/galaxy/commit/e9642720b81b8ef9aed083b49fb2…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-25 (Wed, 25 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
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/menu.js
M static/scripts/layout/page.js
Log Message:
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updating files for real time communication-server and client
Commit: 19d333d427695e11080eee705dc7ad75af5f2cda
https://github.com/galaxyproject/galaxy/commit/19d333d427695e11080eee705dc7…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-26 (Thu, 26 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
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/menu.js
Log Message:
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updated files for real time communication feature addition
Commit: f4273ce56e23be9088b181cf02539be334310cb2
https://github.com/galaxyproject/galaxy/commit/f4273ce56e23be9088b181cf0253…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-26 (Thu, 26 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
updated the chat server client template
Commit: e90de49f584e45cf897fd63cf153dfe1bd251e43
https://github.com/galaxyproject/galaxy/commit/e90de49f584e45cf897fd63cf153…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-27 (Fri, 27 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
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Change you to Me, some style fixes,
Commit: fff6c5e519875588abebd1a649e9097c38df28d6
https://github.com/galaxyproject/galaxy/commit/fff6c5e519875588abebd1a649e9…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-27 (Fri, 27 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
updated chat server for few features
Commit: 053e5173cc9c179e3ad3b55177fd4f91c58839dc
https://github.com/galaxyproject/galaxy/commit/053e5173cc9c179e3ad3b55177fd…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-27 (Fri, 27 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
updating the chat client template
Commit: 574136ce3fc518cfafe7c9e984c35b1cb3036fcd
https://github.com/galaxyproject/galaxy/commit/574136ce3fc518cfafe7c9e984c3…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-27 (Fri, 27 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
style changes
Commit: b7cb80343607d9af997cb539e2c3fe0239ca2ac3
https://github.com/galaxyproject/galaxy/commit/b7cb80343607d9af997cb539e2c3…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
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added show full chat history feature
Commit: a539846c043d79a605eaa847e00557d2662758d1
https://github.com/galaxyproject/galaxy/commit/a539846c043d79a605eaa847e005…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Log Message:
-----------
added show full chat history feature
Commit: 687f26edf706358ef06a84c6f4ae171575d00a69
https://github.com/galaxyproject/galaxy/commit/687f26edf706358ef06a84c6f4ae…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
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updated full chat history feature and added sent date time
Commit: 69d422ca034841b3fef6ede498f3df82f8ccc40b
https://github.com/galaxyproject/galaxy/commit/69d422ca034841b3fef6ede498f3…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
updated chat template code
Commit: 233c752a0b27cbd98aee99b0cb422f6c119f5e4a
https://github.com/galaxyproject/galaxy/commit/233c752a0b27cbd98aee99b0cb42…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
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style changes
Commit: f2ccbc6f6c73786839acb6792c86043337e36ba3
https://github.com/galaxyproject/galaxy/commit/f2ccbc6f6c73786839acb6792c86…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
Log Message:
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style changes and only show the icon if the user has activated the communication app inside of user-preferences
Commit: 67bb0874c522db4c7980032bf15eac2924277a11
https://github.com/galaxyproject/galaxy/commit/67bb0874c522db4c7980032bf15e…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
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add new config parameter to indicate if the communication application is active
Commit: e572be746fc4f93dd3326a41fdd508eaaebe4867
https://github.com/galaxyproject/galaxy/commit/e572be746fc4f93dd3326a41fdd5…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
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Convert "1" also to True inside of string_as_bool()
Commit: cb6f739712d47699ca1196e89d1fea830aeb1868
https://github.com/galaxyproject/galaxy/commit/cb6f739712d47699ca1196e89d1f…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M lib/galaxy/managers/users.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
add user.preferences to be serialised and available in the client
Commit: 1ba0ef705a4d3f3b7538e68a50b9a66d004273cd
https://github.com/galaxyproject/galaxy/commit/1ba0ef705a4d3f3b7538e68a50b9…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
remove debug statements
Commit: e6843de2dfc10fae7d47671d9e3cc7d43ebcbbfd
https://github.com/galaxyproject/galaxy/commit/e6843de2dfc10fae7d47671d9e3c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M templates/user/index.mako
Log Message:
-----------
add new change_communication action to the user controller, to offer communication related options to the user preference panel
Commit: c91c4f4089ec2ffc0195bfcb280fbcf5ea6f755a
https://github.com/galaxyproject/galaxy/commit/c91c4f4089ec2ffc0195bfcb280f…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
A templates/user/communication_settings.mako
Log Message:
-----------
add communication setting to the user preference panel
Commit: b07cfa887d2e751fe35296d8a39749ac73c2deb2
https://github.com/galaxyproject/galaxy/commit/b07cfa887d2e751fe35296d8a397…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M static/maps/layout/menu.js.map
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/menu.js
M static/scripts/layout/page.js
Log Message:
-----------
make client updates
Commit: 1dac71a42ded24fd18db005de003f2fd69a3f551
https://github.com/galaxyproject/galaxy/commit/1dac71a42ded24fd18db005de003…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Merge branch 'rt_comm' of https://github.com/bgruening/galaxy into rt_comm
Commit: 48466e1a84dd5f11e6b4ac03ce657cddf9a49253
https://github.com/galaxyproject/galaxy/commit/48466e1a84dd5f11e6b4ac03ce65…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-28 (Sat, 28 May 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
Log Message:
-----------
adjusted previous changes with new ones for the communication server
Commit: 7ea4051820acf61a176f3a5294957d64f5e2577c
https://github.com/galaxyproject/galaxy/commit/7ea4051820acf61a176f3a529495…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
a lot of cleanups
Commit: 267e1fa3813003f9a18b338a892ce99dddd35a18
https://github.com/galaxyproject/galaxy/commit/267e1fa3813003f9a18b338a892c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
A static/style/base.css
Log Message:
-----------
create symlink
Commit: eb58c101d935fd54e4922f7e5d2e18cc79c61c91
https://github.com/galaxyproject/galaxy/commit/eb58c101d935fd54e4922f7e5d2e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
M scripts/communication_server.py
A scripts/socket.js
Log Message:
-----------
adding socket.js and updating chat server
Commit: 230aa1c106da8f21037f24fa16a5700d54ac9615
https://github.com/galaxyproject/galaxy/commit/230aa1c106da8f21037f24fa16a5…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
R scripts/socket.js
Log Message:
-----------
remove socket.js file
Commit: ee647dbe80d57aa6f596833fdcf2b0ab93b2cf9b
https://github.com/galaxyproject/galaxy/commit/ee647dbe80d57aa6f596833fdcf2…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
revert to fetching resources from the URLs and adjusted the size of chat window
Commit: 7abca061f5dca22b9d6ee9a63f29071f9c5b4c82
https://github.com/galaxyproject/galaxy/commit/7abca061f5dca22b9d6ee9a63f29…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
removed disconnet icon and moved the functionality to online status icon
Commit: 915a882ff492bccbb233d18730c060bccafdd122
https://github.com/galaxyproject/galaxy/commit/915a882ff492bccbb233d18730c0…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-29 (Sun, 29 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
css changes
Commit: 0ef409dc1274af7b1530c3823c1c6a9ca4db21d0
https://github.com/galaxyproject/galaxy/commit/0ef409dc1274af7b1530c3823c1c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-30 (Mon, 30 May 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
adding close button and updating chat ui
Commit: 4491e6bb4765895a979eaaaf22330f5744f7190a
https://github.com/galaxyproject/galaxy/commit/4491e6bb4765895a979eaaaf2233…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-31 (Tue, 31 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
updated server to clean up
Commit: 499f76e1d93bf77aaade47f50c7c1906b8ba31ba
https://github.com/galaxyproject/galaxy/commit/499f76e1d93bf77aaade47f50c7c…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-05-31 (Tue, 31 May 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
removed a couple of fontawesome icons
Commit: 2831ac80f74486d4126b8694e00939af1d69d095
https://github.com/galaxyproject/galaxy/commit/2831ac80f74486d4126b8694e009…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-05 (Sun, 05 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication_server.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
adding feature of chat rooms tabs and notification color
Commit: 656b2c5c6857c32c43c9e3a0ec60224cc4166ca0
https://github.com/galaxyproject/galaxy/commit/656b2c5c6857c32c43c9e3a0ec60…
Author: Remi Marenco <remi.marenco(a)gmail.com>
Date: 2016-06-05 (Sun, 05 Jun 2016)
Changed paths:
A scripts/communication/template/communication.html
M scripts/communication_server.py
Log Message:
-----------
Move the html template into a dedicated folder + Add info about button online/offline
Commit: 5b196571425babf004871390e99ed073b775974f
https://github.com/galaxyproject/galaxy/commit/5b196571425babf004871390e99e…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-06-05 (Sun, 05 Jun 2016)
Changed paths:
A scripts/communication/template/communication.html
M scripts/communication_server.py
Log Message:
-----------
Merge pull request #11 from remimarenco/rt_comm
Add info for connection status + extract HTML into a template folder
Commit: 009cbe4cb4c1c79822ef061c7ed52f07d83ae4bb
https://github.com/galaxyproject/galaxy/commit/009cbe4cb4c1c79822ef061c7ed5…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication/template/communication.html
Log Message:
-----------
added horizontal scroll in case of multiple tabs/rooms
Commit: 7a93c845d6ae4a5a5ce81b484724c7766a31abd4
https://github.com/galaxyproject/galaxy/commit/7a93c845d6ae4a5a5ce81b484724…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Talk to Galaxy to parse cookies
Commit: 03b5622ab5bc3991d13020ff6c8acd533dbe3d05
https://github.com/galaxyproject/galaxy/commit/03b5622ab5bc3991d13020ff6c8a…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Debug mode + flask-login
Commit: ca14290dc95fea6d5b0617659a062f38f92578be
https://github.com/galaxyproject/galaxy/commit/ca14290dc95fea6d5b0617659a06…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Serve separate files using approved serve method
Commit: e08a7cd39a59e191b430dae01e816ab21c8dd11f
https://github.com/galaxyproject/galaxy/commit/e08a7cd39a59e191b430dae01e81…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
A scripts/communication/template/communication.css
M scripts/communication/template/communication.html
A scripts/communication/template/communication.js
M scripts/communication_server.py
Log Message:
-----------
Separate out into three files for legibility
Commit: 346f4e21b039050544fbfbafcc841ebcd9997e17
https://github.com/galaxyproject/galaxy/commit/346f4e21b039050544fbfbafcc84…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Tiny reorg, prettier printing
Commit: c4d11500aca3353bb0c6cdddd92bb0de1712f3b8
https://github.com/galaxyproject/galaxy/commit/c4d11500aca3353bb0c6cdddd92b…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
Refactor to not use client provided usernames
Commit: 67d614e26cf0e8bf138ed9e5172a75dbe9e54aeb
https://github.com/galaxyproject/galaxy/commit/67d614e26cf0e8bf138ed9e5172a…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
Do not trust clients. Also switch to logging from printing
Commit: 8576b634d5f812bd0119f82dcf1cb16e377df68b
https://github.com/galaxyproject/galaxy/commit/8576b634d5f812bd0119f82dcf1c…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-07 (Tue, 07 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
prod ready! (ish)
Commit: d5797fc706c42dc8135cb18d5d7457988a4bbf93
https://github.com/galaxyproject/galaxy/commit/d5797fc706c42dc8135cb18d5d74…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
Whitespace + fix iframe URL
Commit: 640c5b4c7b6eefdb95382e535283609a86a7b452
https://github.com/galaxyproject/galaxy/commit/640c5b4c7b6eefdb95382e535283…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
A scripts/communication/template/communication.css
M scripts/communication/template/communication.html
A scripts/communication/template/communication.js
M scripts/communication_server.py
Log Message:
-----------
Merge pull request #12 from erasche/rt-comm-2
Some small updates for security
Commit: 983328f817ff9da469df1000adc92367b455b015
https://github.com/galaxyproject/galaxy/commit/983328f817ff9da469df1000adc9…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M scripts/communication_server.py
Log Message:
-----------
change handling of id_secret slightly
Commit: 0bff02f95ddd19d5cd22ca9a70ca316913fd0f3d
https://github.com/galaxyproject/galaxy/commit/0bff02f95ddd19d5cd22ca9a70ca…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
A scripts/communication/communication_server.py
R scripts/communication_server.py
Log Message:
-----------
move everything under scripts/communication
Commit: a4970e71cf04acf336c4463c0103a7aa0f8de777
https://github.com/galaxyproject/galaxy/commit/a4970e71cf04acf336c4463c0103…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
adjust path to galaxy-lib
Commit: c79dadd931cdb989197ac78096b98c4163725568
https://github.com/galaxyproject/galaxy/commit/c79dadd931cdb989197ac78096b9…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
client updates
Commit: 4d186982ce9fb907d9d25006dc7646e14e589d32
https://github.com/galaxyproject/galaxy/commit/4d186982ce9fb907d9d25006dc76…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
fix a few bugs, we should now be back to buisness
Commit: 3dbd6d8074c44d7cfb333c8b5a49de40e683af9a
https://github.com/galaxyproject/galaxy/commit/3dbd6d8074c44d7cfb333c8b5a49…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
Log Message:
-----------
fix error if no user is logged in
Commit: 5a3580c752c45e5a7d68fd742a0b6336a09169ea
https://github.com/galaxyproject/galaxy/commit/5a3580c752c45e5a7d68fd742a0b…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
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
Log Message:
-----------
client updates
Commit: 6bc64e74263097a969b5d097c9334b41b7b59425
https://github.com/galaxyproject/galaxy/commit/6bc64e74263097a969b5d097c933…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-08 (Wed, 08 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
enhance documentation
Commit: 74e3e05034e146bfa3b13c177557e78097265bb7
https://github.com/galaxyproject/galaxy/commit/74e3e05034e146bfa3b13c177557…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-09 (Thu, 09 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
fix js bug
Commit: 043b129c91b3b2b679d4bb4e31db4970c26219e8
https://github.com/galaxyproject/galaxy/commit/043b129c91b3b2b679d4bb4e31db…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-09 (Thu, 09 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
Merge branch 'rt_comm' of https://github.com/bgruening/galaxy into rt_comm
Commit: 0cd28c72515804f859cb9054a13a157fc8ebf2e6
https://github.com/galaxyproject/galaxy/commit/0cd28c72515804f859cb9054a13a…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
-----------
Added global chat rooms
Commit: 581108a442ec762dc9d87111f9425c01accc67c5
https://github.com/galaxyproject/galaxy/commit/581108a442ec762dc9d87111f942…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
backend work for persistent chat rooms
Commit: f75189aaaadf697d5759023cdc72fefa8f1d17c8
https://github.com/galaxyproject/galaxy/commit/f75189aaaadf697d5759023cdc72…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-10 (Fri, 10 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
style cleanups
Commit: e0c4e1cef04cde226bc140a62beb47670a25b85d
https://github.com/galaxyproject/galaxy/commit/e0c4e1cef04cde226bc140a62beb…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-11 (Sat, 11 Jun 2016)
Changed paths:
M lib/galaxy/managers/configuration.py
Log Message:
-----------
access the list of persistent chat rooms via Galaxy.config object
Commit: 80ee76cb39c06f8a922e3fbcf9930711c3eeb6ce
https://github.com/galaxyproject/galaxy/commit/80ee76cb39c06f8a922e3fbcf993…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-11 (Sat, 11 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Adding persistent rooms from config
Commit: 074fefeda2b10accec700e250e516aa8bd9e6a0b
https://github.com/galaxyproject/galaxy/commit/074fefeda2b10accec700e250e51…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-13 (Mon, 13 Jun 2016)
Changed paths:
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
-----------
Adding features-space enabled chat room names, ctrl+l for chat log deletion, removing delete icon, smooth transition on window load and code cleanup
Commit: f034f1778b7482e182f8a03d6c53774361875b56
https://github.com/galaxyproject/galaxy/commit/f034f1778b7482e182f8a03d6c53…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-14 (Tue, 14 Jun 2016)
Changed paths:
M scripts/communication/template/communication.css
M scripts/communication/template/communication.js
Log Message:
-----------
make the communication window more packed
Commit: 111a1c62223d4d252f91f5bed5f009bf3c58bd2e
https://github.com/galaxyproject/galaxy/commit/111a1c62223d4d252f91f5bed5f0…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-14 (Tue, 14 Jun 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Fixing the issue with persistent room names with spaces, adding fancy scroll bar, buttons instead of links for persistent rooms and UI changes for message area
Commit: 5ed647e34f69fb3ab05982a135fa2be7f65310f5
https://github.com/galaxyproject/galaxy/commit/5ed647e34f69fb3ab05982a135fa…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
release preparation
Commit: f27e80e46dd1a1af7991fe1fc62a428dbbe49715
https://github.com/galaxyproject/galaxy/commit/f27e80e46dd1a1af7991fe1fc62a…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
fix documenation
Commit: 52e1918e9e2807f30c0c5a64d9493d5a766f6312
https://github.com/galaxyproject/galaxy/commit/52e1918e9e2807f30c0c5a64d949…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
add
Commit: b18decddda86ddc0fa7a813c1bad64722123da83
https://github.com/galaxyproject/galaxy/commit/b18decddda86ddc0fa7a813c1bad…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
client updates
Commit: b8a92a3f80661f2b729160163343034216616e53
https://github.com/galaxyproject/galaxy/commit/b8a92a3f80661f2b729160163343…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
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Fixing issue with no persistent rooms
Commit: ab43e094c2c7f5d3c5ba6d2e82af3f7c5fd52970
https://github.com/galaxyproject/galaxy/commit/ab43e094c2c7f5d3c5ba6d2e82af…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
Allow changing settings under remote_user
Commit: 83e61f1ca4c16b5383b7ae0dba36c1b0aab2dce8
https://github.com/galaxyproject/galaxy/commit/83e61f1ca4c16b5383b7ae0dba36…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
-----------
Support gravatar and rework template
Commit: 0d9865b5c56c1d6e7d0f15c8e566e1b30fffd2f3
https://github.com/galaxyproject/galaxy/commit/0d9865b5c56c1d6e7d0f15c8e566…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-06-18 (Sat, 18 Jun 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
M scripts/communication/communication_server.py
M scripts/communication/template/communication.css
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
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Merge pull request #14 from erasche/rt_comm-gravatar
Gravatar suppot
Commit: 4a304b63b12073dc2c82e811fa9acde04337170b
https://github.com/galaxyproject/galaxy/commit/4a304b63b12073dc2c82e811fa9a…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/communication_server.py
Log Message:
-----------
fix pep8
Commit: b690abb46a03c1d622e8395ae6d4752952354861
https://github.com/galaxyproject/galaxy/commit/b690abb46a03c1d622e8395ae6d4…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
make chat view a little bit more compact and fix bug in displaying "me" messages
Commit: c017b516663a312a866fd3000547982838a67b8a
https://github.com/galaxyproject/galaxy/commit/c017b516663a312a866fd3000547…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.css
M scripts/communication/template/communication.js
Log Message:
-----------
Fixed UI issues and log deletion functionality in main tab
Commit: e477d728d407cde21449549c5e464da8b54044f0
https://github.com/galaxyproject/galaxy/commit/e477d728d407cde21449549c5e46…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
do not show gravatar for server messages
Commit: 10c2764f097beb1b5c2b221377424002c698d7ca
https://github.com/galaxyproject/galaxy/commit/10c2764f097beb1b5c2b22137742…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
add the identicon to gravatar
Commit: feb00567e4f08970be67f75ccee8df7940b9067a
https://github.com/galaxyproject/galaxy/commit/feb00567e4f08970be67f75ccee8…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.css
M scripts/communication/template/communication.js
Log Message:
-----------
Adjusted the vertical position of gravatar icons
Commit: 008220d88d4d2699f901b9e2e656afd7510473c0
https://github.com/galaxyproject/galaxy/commit/008220d88d4d2699f901b9e2e656…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.js
Log Message:
-----------
Adjusted the vertical position of gravatar icons
Commit: 464e9a42615bed11197a43fbd082f0c31076ca71
https://github.com/galaxyproject/galaxy/commit/464e9a42615bed11197a43fbd082…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M scripts/communication/template/communication.html
M scripts/communication/template/communication.js
Log Message:
-----------
Fixed issue with Firefox auto scrolling
Commit: 1f1c35f70873b87e0923fc04b1c11d546e100a04
https://github.com/galaxyproject/galaxy/commit/1f1c35f70873b87e0923fc04b1c1…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M .gitignore
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/users.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A scripts/communication/communication_server.py
A scripts/communication/template/communication.css
A scripts/communication/template/communication.html
A scripts/communication/template/communication.js
M static/maps/layout/menu.js.map
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/menu.js
M static/scripts/layout/page.js
A static/style/base.css
A templates/user/communication_settings.mako
M templates/user/index.mako
Log Message:
-----------
merge
Commit: 474a8889e346b21f24d557880929b9c0eb989a8a
https://github.com/galaxyproject/galaxy/commit/474a8889e346b21f24d557880929…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
update client
Commit: b81034554377d3e0a3f971eae579c42a032c0685
https://github.com/galaxyproject/galaxy/commit/b81034554377d3e0a3f971eae579…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-06-19 (Sun, 19 Jun 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
fix pep8 warning
Commit: 93c33b4188548ff4575befcbb5b7787585085364
https://github.com/galaxyproject/galaxy/commit/93c33b4188548ff4575befcbb5b7…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-10 (Sun, 10 Jul 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/style/less/base.less
M static/maps/layout/menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/style/blue/base.css
Log Message:
-----------
A bit of clean of menu.js for the chat tab
Commit: 66c3e418a6d55fbee8211a95fb0913e7e0418b17
https://github.com/galaxyproject/galaxy/commit/66c3e418a6d55fbee8211a95fb09…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-10 (Sun, 10 Jul 2016)
Changed paths:
A client/galaxy/scripts/layout/generic-nav-view.js
Log Message:
-----------
Adding generic nav view
Commit: ff23df05216750b5df4c7f2050fe30f009d24832
https://github.com/galaxyproject/galaxy/commit/ff23df05216750b5df4c7f2050fe…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-10 (Sun, 10 Jul 2016)
Changed paths:
M static/maps/layout/menu.js.map
Log Message:
-----------
adding static menu map file
Commit: 28744e1235a0decc26f2fb5545f4946e6cece25a
https://github.com/galaxyproject/galaxy/commit/28744e1235a0decc26f2fb5545f4…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-07-10 (Sun, 10 Jul 2016)
Changed paths:
M .gitignore
Log Message:
-----------
ignore IDEA files
Commit: 0d915ce131e1928fe1feab82633ef6bf90ebce0f
https://github.com/galaxyproject/galaxy/commit/0d915ce131e1928fe1feab82633e…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2016-07-14 (Thu, 14 Jul 2016)
Changed paths:
M client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/style/less/base.less
M scripts/communication/template/communication.css
M scripts/communication/template/communication.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Adding maximize/minimize feature to the communication channel
Commit: 5b0641fe4a5dc681b75a357f04578f7b53ccb733
https://github.com/galaxyproject/galaxy/commit/5b0641fe4a5dc681b75a357f0457…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M .ci/py3_sources.txt
M Makefile
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/ui.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/library/datasets.js
M config/plugins/visualizations/charts/static/library/jobs.js
M config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/library/ui-table-form.js
M config/plugins/visualizations/charts/static/models/chart.js
M config/plugins/visualizations/charts/static/models/config.js
R config/plugins/visualizations/charts/static/models/group.js
R config/plugins/visualizations/charts/static/models/groups.js
M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
M config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/group.js
A config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/graphviz/config/graphviz.xml
M config/plugins/visualizations/graphviz/static/js/graphVis.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/visualizations/graphviz/templates/graphviz.mako
M config/tool_data_table_conf.xml.sample
A config/tool_destinations.yml.sample
A display_applications/igv/bigwig.xml
A display_applications/ucsc/trackhub.xml
A doc/source/admin/grt.rst
M doc/source/admin/index.rst
M doc/source/admin/interactive_environments.rst
M doc/source/dev/index.rst
A doc/source/dev/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/actions/post.py
A lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M run_tests.sh
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/drmaa_external_runner.py
M scripts/fetch_eggs.py
A scripts/grt.py
A scripts/grt.yml.sample
M scripts/set_dataset_sizes.py
M setup.cfg
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-template.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-template.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M templates/admin/impersonate.mako
M templates/ind_share_base.mako
M templates/user/change_password.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/history/grid.mako
M templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
M test/api/helpers.py
M test/api/test_datasets.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
A test/functional/tools/identifier_collection.xml
A test/functional/tools/output_filter_exception_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional_tests.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
A test/unit/datatypes/test_data.py
A test/unit/jobs/dynamic_tool_destination/__init__.py
A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml
A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/data/test.empty
A test/unit/jobs/dynamic_tool_destination/data/test.fasta
A test/unit/jobs/dynamic_tool_destination/data/test1.full
A test/unit/jobs/dynamic_tool_destination/data/test3.full
A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
A test/unit/jobs/dynamic_tool_destination/data/test_users.yml
A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
A test/unit/jobs/dynamic_tool_destination/ymltests.py
M test/unit/managers/base.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_toolbox.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/gsummary.xml
M tox.ini
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
Commit: 6b8b0cde5b6a2725177e409ebc84ba1591f5bd40
https://github.com/galaxyproject/galaxy/commit/6b8b0cde5b6a2725177e409ebc84…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-07-22 (Fri, 22 Jul 2016)
Changed paths:
M .ci/py3_sources.txt
M Makefile
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/ui.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/library/datasets.js
M config/plugins/visualizations/charts/static/library/jobs.js
M config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/library/ui-table-form.js
M config/plugins/visualizations/charts/static/models/chart.js
M config/plugins/visualizations/charts/static/models/config.js
R config/plugins/visualizations/charts/static/models/group.js
R config/plugins/visualizations/charts/static/models/groups.js
M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
M config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/group.js
A config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/graphviz/config/graphviz.xml
M config/plugins/visualizations/graphviz/static/js/graphVis.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/visualizations/graphviz/templates/graphviz.mako
M config/tool_data_table_conf.xml.sample
A config/tool_destinations.yml.sample
A display_applications/igv/bigwig.xml
A display_applications/ucsc/trackhub.xml
A doc/source/admin/grt.rst
M doc/source/admin/index.rst
M doc/source/admin/interactive_environments.rst
M doc/source/dev/index.rst
A doc/source/dev/interactive_environments.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/actions/post.py
A lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M run_tests.sh
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/drmaa_external_runner.py
M scripts/fetch_eggs.py
A scripts/grt.py
A scripts/grt.yml.sample
M scripts/set_dataset_sizes.py
M setup.cfg
A static/maps/layout/generic-nav-view.js.map
M static/maps/mvc/collection/collection-li.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-template.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.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
A static/scripts/layout/generic-nav-view.js
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-template.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M templates/admin/impersonate.mako
M templates/ind_share_base.mako
M templates/user/change_password.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/history/grid.mako
M templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
M test/api/helpers.py
M test/api/test_datasets.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
A test/functional/tools/identifier_collection.xml
A test/functional/tools/output_filter_exception_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional_tests.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
A test/unit/datatypes/test_data.py
A test/unit/jobs/dynamic_tool_destination/__init__.py
A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml
A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/data/test.empty
A test/unit/jobs/dynamic_tool_destination/data/test.fasta
A test/unit/jobs/dynamic_tool_destination/data/test1.full
A test/unit/jobs/dynamic_tool_destination/data/test3.full
A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
A test/unit/jobs/dynamic_tool_destination/data/test_users.yml
A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
A test/unit/jobs/dynamic_tool_destination/ymltests.py
M test/unit/managers/base.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_toolbox.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/gsummary.xml
M tox.ini
Log Message:
-----------
make client
Commit: b0566ad9ce8daf42a10bd013f7bd5d9efdfc4fa4
https://github.com/galaxyproject/galaxy/commit/b0566ad9ce8daf42a10bd013f7bd…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-07-23 (Sat, 23 Jul 2016)
Changed paths:
M .gitignore
A client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/style/less/base.less
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/users.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A scripts/communication/communication_server.py
A scripts/communication/template/communication.css
A scripts/communication/template/communication.html
A scripts/communication/template/communication.js
A static/maps/layout/generic-nav-view.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/page.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/layout/generic-nav-view.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
A static/style/base.css
M static/style/blue/base.css
A templates/user/communication_settings.mako
M templates/user/index.mako
Log Message:
-----------
Merge pull request #2515 from bgruening/realtime_communication
Add a simple Galaxy Communication Server for realtime communication between Galaxy users.
Compare: https://github.com/galaxyproject/galaxy/compare/47522208c6d7...b0566ad9ce8d
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