Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 85aaa23785ff10337b40d9a5f4316e8a4683668d
https://github.com/galaxyproject/galaxy/commit/85aaa23785ff10337b40d9a5f431…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Make conda install and resolver status more robust
We disable the conda resolver if conda_exec is not found and we are
unable to install conda. Skip installing conda if it won't be used
(because conda exec is outside of conda_prefix).
Install conda if conda_prefix is an empty directory.
Commit: fdc43a1448453afa1e65ae43f20b71865762882d
https://github.com/galaxyproject/galaxy/commit/fdc43a1448453afa1e65ae43f20b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Rephrase conda options and explain conda_prefix, add current length limitation
Commit: 0cc10d184dfb949130fefedfe12258241f4982c9
https://github.com/galaxyproject/galaxy/commit/0cc10d184dfb949130fefedfe122…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Move can_install_conda and is_conda_installed into CondaContext
Commit: 30a14e3c392395805453f15d35b9d9c0b76a65ee
https://github.com/galaxyproject/galaxy/commit/30a14e3c392395805453f15d35b9…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Raise a more specific exception
Commit: 40f8589c3830af3c4ca69ebcd394d9bf5a53e65b
https://github.com/galaxyproject/galaxy/commit/40f8589c3830af3c4ca69ebcd394…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #2789 from mvdbeek/is_conda_installed
Make conda install and resolver status more robust
Compare: https://github.com/galaxyproject/galaxy/compare/d87fbdd5b80b...40f8589c3830
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: af533a7a6ff0106185350466b31153e40c394389
https://github.com/galaxyproject/galaxy/commit/af533a7a6ff0106185350466b311…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-08-11 (Thu, 11 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/queues.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/util/postfork.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
Log Message:
-----------
Create a uWSGI postfork function registry. Also, start the tool conf
watcher thread post-fork.
Commit: 7ebf7e57063624758eaea62756126fd556cfa989
https://github.com/galaxyproject/galaxy/commit/7ebf7e57063624758eaea6275612…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/update_repository_manager.py
Log Message:
-----------
Force update repository manager to launch postfork.
Commit: 7c5cadbe7dc81423821d0809451ad5e2fdb8d53a
https://github.com/galaxyproject/galaxy/commit/7c5cadbe7dc81423821d0809451a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add debugging to indicate running threads just prior to prefork, to make finding and fixing of these easier in the future.
Commit: fb6f3c9c698a14d9f67fe6262e16c65ddc78477e
https://github.com/galaxyproject/galaxy/commit/fb6f3c9c698a14d9f67fe6262e16…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M client/galaxy/style/less/library.less
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
separate styles of new and old libs fixing various ui bugs
Commit: 0719d83837aacf45b200709cb7b243badca87488
https://github.com/galaxyproject/galaxy/commit/0719d83837aacf45b200709cb7b2…
Author: Carl Eberhard <carlfeberhard(a)users.noreply.github.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M client/galaxy/style/less/library.less
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
Merge pull request #2780 from martenson/lib-style-fix
[16.07] separate styles of new and old libraries fixing various ui bugs
Commit: efbd8f2d9fd68dac5039ae21dedb1be1e5cd23bc
https://github.com/galaxyproject/galaxy/commit/efbd8f2d9fd68dac5039ae21dedb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/util/postfork.py
Log Message:
-----------
Separates the decorator from the injected uwsgi package to fix
'process_is_uwsgi' logic.
Commit: 2f0c4562ae3314caa58c7ff1b87ecbd34c485966
https://github.com/galaxyproject/galaxy/commit/2f0c4562ae3314caa58c7ff1b87e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/util/postfork.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
Log Message:
-----------
Merge pull request #4 from dannon/uwsgi-fork
Force update repository manager to launch postfork.
Commit: 699e955d7f3bde9744d6a6cc0b0d2ec73eaa03bd
https://github.com/galaxyproject/galaxy/commit/699e955d7f3bde9744d6a6cc0b0d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/util/postfork.py
Log Message:
-----------
Add a warning when it is detected that a process is uwsgi based but uwsgidecorators is not available.
Commit: be7c5bce1d93dfe5ab28f3176488f32400d7e415
https://github.com/galaxyproject/galaxy/commit/be7c5bce1d93dfe5ab28f3176488…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/util/postfork.py
Log Message:
-----------
Words.
Commit: 6ca6f9019ee034550d8da1eedfa66619bce0e584
https://github.com/galaxyproject/galaxy/commit/6ca6f9019ee034550d8da1eedfa6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/util/postfork.py
Log Message:
-----------
Merge pull request #5 from dannon/uwsgi-fork
Add a warning when it is detected that a process is uwsgi based but u…
Commit: d87fbdd5b80b110d3f0a0f8805b63eb2246a28cb
https://github.com/galaxyproject/galaxy/commit/d87fbdd5b80b110d3f0a0f8805b6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/queues.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/util/postfork.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
Log Message:
-----------
Merge pull request #2774 from natefoo/uwsgi-fork
[16.07] Create a uWSGI postfork function registry and start the tool conf watcher thread post-fork
Commit: 62d69be1565d8d854fe8bd0a289732ec9e12001c
https://github.com/galaxyproject/galaxy/commit/62d69be1565d8d854fe8bd0a2897…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M client/galaxy/style/less/library.less
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/queues.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/util/postfork.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
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/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
Merge branch 'release_16.07' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/d20828b685e5...62d69be1565d
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: af533a7a6ff0106185350466b31153e40c394389
https://github.com/galaxyproject/galaxy/commit/af533a7a6ff0106185350466b311…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-08-11 (Thu, 11 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/queues.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/util/postfork.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
Log Message:
-----------
Create a uWSGI postfork function registry. Also, start the tool conf
watcher thread post-fork.
Commit: 7ebf7e57063624758eaea62756126fd556cfa989
https://github.com/galaxyproject/galaxy/commit/7ebf7e57063624758eaea6275612…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/update_repository_manager.py
Log Message:
-----------
Force update repository manager to launch postfork.
Commit: 7c5cadbe7dc81423821d0809451ad5e2fdb8d53a
https://github.com/galaxyproject/galaxy/commit/7c5cadbe7dc81423821d0809451a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add debugging to indicate running threads just prior to prefork, to make finding and fixing of these easier in the future.
Commit: efbd8f2d9fd68dac5039ae21dedb1be1e5cd23bc
https://github.com/galaxyproject/galaxy/commit/efbd8f2d9fd68dac5039ae21dedb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/util/postfork.py
Log Message:
-----------
Separates the decorator from the injected uwsgi package to fix
'process_is_uwsgi' logic.
Commit: 2f0c4562ae3314caa58c7ff1b87ecbd34c485966
https://github.com/galaxyproject/galaxy/commit/2f0c4562ae3314caa58c7ff1b87e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/util/postfork.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
Log Message:
-----------
Merge pull request #4 from dannon/uwsgi-fork
Force update repository manager to launch postfork.
Commit: 699e955d7f3bde9744d6a6cc0b0d2ec73eaa03bd
https://github.com/galaxyproject/galaxy/commit/699e955d7f3bde9744d6a6cc0b0d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/util/postfork.py
Log Message:
-----------
Add a warning when it is detected that a process is uwsgi based but uwsgidecorators is not available.
Commit: be7c5bce1d93dfe5ab28f3176488f32400d7e415
https://github.com/galaxyproject/galaxy/commit/be7c5bce1d93dfe5ab28f3176488…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/util/postfork.py
Log Message:
-----------
Words.
Commit: 6ca6f9019ee034550d8da1eedfa66619bce0e584
https://github.com/galaxyproject/galaxy/commit/6ca6f9019ee034550d8da1eedfa6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/util/postfork.py
Log Message:
-----------
Merge pull request #5 from dannon/uwsgi-fork
Add a warning when it is detected that a process is uwsgi based but u…
Commit: d87fbdd5b80b110d3f0a0f8805b63eb2246a28cb
https://github.com/galaxyproject/galaxy/commit/d87fbdd5b80b110d3f0a0f8805b6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/queues.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/util/postfork.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
Log Message:
-----------
Merge pull request #2774 from natefoo/uwsgi-fork
[16.07] Create a uWSGI postfork function registry and start the tool conf watcher thread post-fork
Compare: https://github.com/galaxyproject/galaxy/compare/0719d83837aa...d87fbdd5b80b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 87038d275acf46d84c1c8c110742a44002b6bdf3
https://github.com/galaxyproject/galaxy/commit/87038d275acf46d84c1c8c110742…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M lib/galaxy/workflow/modules.py
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Ensure proper filtering of dataset when injecting input data on workflow initialization
Commit: e614a6e6e4300d361d8b861a733e312f82e59b5a
https://github.com/galaxyproject/galaxy/commit/e614a6e6e4300d361d8b861a733e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M lib/galaxy/workflow/modules.py
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Improve initial value injection, adjust former run form
Commit: 6fb006c460daca657a429ae78e63add6c48ef151
https://github.com/galaxyproject/galaxy/commit/6fb006c460daca657a429ae78e63…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-15 (Mon, 15 Aug 2016)
Changed paths:
M lib/galaxy/workflow/modules.py
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Merge pull request #2777 from guerler/fix_filter_set
Ensure proper filtering of dataset when injecting input data on workflow initialization
Compare: https://github.com/galaxyproject/galaxy/compare/3b848891e5cf...6fb006c460da
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: fb6f3c9c698a14d9f67fe6262e16c65ddc78477e
https://github.com/galaxyproject/galaxy/commit/fb6f3c9c698a14d9f67fe6262e16…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M client/galaxy/style/less/library.less
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
separate styles of new and old libs fixing various ui bugs
Commit: 0719d83837aacf45b200709cb7b243badca87488
https://github.com/galaxyproject/galaxy/commit/0719d83837aacf45b200709cb7b2…
Author: Carl Eberhard <carlfeberhard(a)users.noreply.github.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M client/galaxy/style/less/library.less
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
M static/style/blue/library.css
Log Message:
-----------
Merge pull request #2780 from martenson/lib-style-fix
[16.07] separate styles of new and old libraries fixing various ui bugs
Compare: https://github.com/galaxyproject/galaxy/compare/66e725b6e33b...0719d83837aa
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b2593f0ff209aaef80b82caec4ea7c8018091e87
https://github.com/galaxyproject/galaxy/commit/b2593f0ff209aaef80b82caec4ea…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 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:
-----------
Properly refresh history contents after submitting workflow through new scheduler
Commit: 0dee01934a9f3e4cb62e005b07a3442dd815572d
https://github.com/galaxyproject/galaxy/commit/0dee01934a9f3e4cb62e005b07a3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 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:
-----------
Merge pull request #2776 from guerler/properly_refresh_after_workflow
Properly refresh history contents after submitting workflow through api scheduler
Compare: https://github.com/galaxyproject/galaxy/compare/0692f8b4b11d...0dee01934a9f