Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4431d735c8908b19bbcd1ca594ec1a194cf4d299
https://github.com/galaxyproject/galaxy/commit/4431d735c8908b19bbcd1ca594ec…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-12-08 (Thu, 08 Dec 2016)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
Log Message:
-----------
Extend list of tabular datatypes for bar diagrams
Commit: 22687410c4829dd9a0e44f55ee93b1020c8eab20
https://github.com/galaxyproject/galaxy/commit/22687410c4829dd9a0e44f55ee93…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-09 (Fri, 09 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Ensure Conda prefix and cached environment are absolute paths
Otherwise when Conda commands are executed from the job working
directory, they will break.
Commit: 879e3d69606e1a4b98bd34f75bf905b9da6edcfa
https://github.com/galaxyproject/galaxy/commit/879e3d69606e1a4b98bd34f75bf9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-09 (Fri, 09 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Skip building cache if force_rebuild is False
Also:
- re-raise exception if rmtree() fails
- change hash(ed)_requirements to hash(ed)_dependencies
Commit: 7c9d9d2231ecc113f7d69737a4aa4ec140b7e48c
https://github.com/galaxyproject/galaxy/commit/7c9d9d2231ecc113f7d69737a4aa…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-09 (Fri, 09 Dec 2016)
Changed paths:
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Apply a fix similar to 36134bca694c9dc6b2584fb661dfbce4ddb793e6 for the workflow editor. Not ideal, but this is old code we're replacing as the editor is overhauled.
Commit: 5a7f9e876e28ea773b79af9bbb887de7cff4aaa7
https://github.com/galaxyproject/galaxy/commit/5a7f9e876e28ea773b79af9bbb88…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Correctly update TS repo status
Execute build_dependency_cache() only if using a cached dependency
manager.
Set tool versions only if the TS repo contains tools.
Raise exception if fetch_tool_versions() fails, previously the
error message never reached the UI.
Commit: 9dda310cd35e18c3ef86c5b09a021fc359fe5011
https://github.com/galaxyproject/galaxy/commit/9dda310cd35e18c3ef86c5b09a02…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge pull request #3296 from dannon/workflow_editor_toolsearch_messagebox_fix
[16.10] Workflow editor 'messagebox' fix.
Commit: 22c7fcf3fff19ed9f271ada3cd8c007a96444768
https://github.com/galaxyproject/galaxy/commit/22c7fcf3fff19ed9f271ada3cd8c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Merge pull request #3295 from nsoranzo/release_16.10_tool_install_fixes
[16.10] Tool install fixes
Commit: 2c833499b130aca72ab78d112692f2a9f0d4d9e6
https://github.com/galaxyproject/galaxy/commit/2c833499b130aca72ab78d112692…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
Log Message:
-----------
Merge pull request #3287 from guerler/fix_chart_datatypes
[16.10] Rely on tabular subclass matching through vizframework layer
Commit: 584114a4698076b79d77124b27867d6ea2386188
https://github.com/galaxyproject/galaxy/commit/584114a4698076b79d77124b2786…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-12 (Mon, 12 Dec 2016)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/tool_shed/galaxy_install/install_manager.py
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge branch 'release_16.10' into dev
Conflicts:
config/plugins/visualizations/charts/static/repository/build/registry.js
config/plugins/visualizations/charts/static/repository/build/registry.js.map
Compare: https://github.com/galaxyproject/galaxy/compare/c7568a1d871b...584114a46980
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 28c2acf17dfc2b73276de0ba7cb73c93d730dde5
https://github.com/galaxyproject/galaxy/commit/28c2acf17dfc2b73276de0ba7cb7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-12 (Mon, 12 Dec 2016)
Changed paths:
M Makefile
Log Message:
-----------
Adds a 'make charts' makefile target to make it more obvious how to
build these. Not invoked automatically though, since these should very
rarely conflict and we don't want to have version build difference
conflicts (harmless) all the time.
Commit: 8eba2f2f1bbc32a97eb51b97712fb67691723282
https://github.com/galaxyproject/galaxy/commit/8eba2f2f1bbc32a97eb51b97712f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-12 (Mon, 12 Dec 2016)
Changed paths:
M config/plugins/visualizations/charts/webpack.config.js
Log Message:
-----------
Remove unnecessary require -- webpack is expected as the executor here
Commit: a0ae63d8c2983f17aa75b161bd25fa505af20a6c
https://github.com/galaxyproject/galaxy/commit/a0ae63d8c2983f17aa75b161bd25…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-12 (Mon, 12 Dec 2016)
Changed paths:
M Makefile
Log Message:
-----------
Set NODE_MODULES var for 'grunt charts', required due to the execution model here.
Commit: 49cdd7082d86c07ab07bb1bee8e4b26baf6b4eb8
https://github.com/galaxyproject/galaxy/commit/49cdd7082d86c07ab07bb1bee8e4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-12 (Mon, 12 Dec 2016)
Changed paths:
M Makefile
Log Message:
-----------
Shot in the dark at @nsoranzo's build woes.
Commit: 015c32854f2d9ff9402b73f9fe8b291cd2346df5
https://github.com/galaxyproject/galaxy/commit/015c32854f2d9ff9402b73f9fe8b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-12 (Mon, 12 Dec 2016)
Changed paths:
M Makefile
Log Message:
-----------
Override possible env var use which can break this -- we always want to use Galaxy's modules here anyway
Commit: c7568a1d871b8c4c3816130c33a24e1e21e12f29
https://github.com/galaxyproject/galaxy/commit/c7568a1d871b8c4c3816130c33a2…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-12-12 (Mon, 12 Dec 2016)
Changed paths:
M Makefile
M config/plugins/visualizations/charts/webpack.config.js
Log Message:
-----------
Merge pull request #3306 from dannon/charts_makefile_target
Adds a 'make charts' makefile target to make it more obvious how to build these.
Compare: https://github.com/galaxyproject/galaxy/compare/fc5ac197914b...c7568a1d871b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 96bd4552e1b1a7b18d57f8e0d0f1a5da22b085a1
https://github.com/galaxyproject/galaxy/commit/96bd4552e1b1a7b18d57f8e0d0f1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/sniff.py
Log Message:
-----------
Further tighten up GG format.
I encountered similar input problems to #864 - this helps a little.
- Ensure first column is a valid marker as outlined on https://genome.ucsc.edu/goldenpath/help/hgGenomeHelp.html.
- Avoid readlines() since it may allocate huge amounts on memory on certain inputs.
- Eliminate bare exception.
Rebased with bug fixes in original commit and better testing and tighter exception handling as suggested by @nsoranzo.
Commit: 176d4d5cf49a5859357ba88f38ef6a2136fb8570
https://github.com/galaxyproject/galaxy/commit/176d4d5cf49a5859357ba88f38ef…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-12 (Mon, 12 Dec 2016)
Changed paths:
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/sniff.py
Log Message:
-----------
Merge pull request #3233 from jmchilton/gg_datatype
Further tighten up GG format.
Compare: https://github.com/galaxyproject/galaxy/compare/e6374bfc211f...176d4d5cf49a
Branch: refs/heads/release_16.10
Home: https://github.com/galaxyproject/galaxy
Commit: 4431d735c8908b19bbcd1ca594ec1a194cf4d299
https://github.com/galaxyproject/galaxy/commit/4431d735c8908b19bbcd1ca594ec…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-12-08 (Thu, 08 Dec 2016)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
Log Message:
-----------
Extend list of tabular datatypes for bar diagrams
Commit: 2c833499b130aca72ab78d112692f2a9f0d4d9e6
https://github.com/galaxyproject/galaxy/commit/2c833499b130aca72ab78d112692…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
Log Message:
-----------
Merge pull request #3287 from guerler/fix_chart_datatypes
[16.10] Rely on tabular subclass matching through vizframework layer
Compare: https://github.com/galaxyproject/galaxy/compare/22c7fcf3fff1...2c833499b130
Branch: refs/heads/release_16.10
Home: https://github.com/galaxyproject/galaxy
Commit: 22687410c4829dd9a0e44f55ee93b1020c8eab20
https://github.com/galaxyproject/galaxy/commit/22687410c4829dd9a0e44f55ee93…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-09 (Fri, 09 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Ensure Conda prefix and cached environment are absolute paths
Otherwise when Conda commands are executed from the job working
directory, they will break.
Commit: 879e3d69606e1a4b98bd34f75bf905b9da6edcfa
https://github.com/galaxyproject/galaxy/commit/879e3d69606e1a4b98bd34f75bf9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-09 (Fri, 09 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Skip building cache if force_rebuild is False
Also:
- re-raise exception if rmtree() fails
- change hash(ed)_requirements to hash(ed)_dependencies
Commit: 5a7f9e876e28ea773b79af9bbb887de7cff4aaa7
https://github.com/galaxyproject/galaxy/commit/5a7f9e876e28ea773b79af9bbb88…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Correctly update TS repo status
Execute build_dependency_cache() only if using a cached dependency
manager.
Set tool versions only if the TS repo contains tools.
Raise exception if fetch_tool_versions() fails, previously the
error message never reached the UI.
Commit: 22c7fcf3fff19ed9f271ada3cd8c007a96444768
https://github.com/galaxyproject/galaxy/commit/22c7fcf3fff19ed9f271ada3cd8c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Merge pull request #3295 from nsoranzo/release_16.10_tool_install_fixes
[16.10] Tool install fixes
Compare: https://github.com/galaxyproject/galaxy/compare/9dda310cd35e...22c7fcf3fff1