Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bbc403b2e1411f2a54fe3c28283dbd26dddbc780 https://github.com/galaxyproject/galaxy/commit/bbc403b2e1411f2a54fe3c28283db... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-23 (Wed, 23 Nov 2016)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Add cached dependency manager

Similar to https://github.com/galaxyproject/galaxy/pull/2986, implement a mechanism that allows tool dependencies to be cached.

If the `use_cached_dependency_manager` option is set to True in galaxy.ini, we build a hash of the combination of a tools' requirements, and store the resulting environment in a directory specified by the `tool_dependency_cache_dir` option in galaxy.ini.

Commit: 185856f6afd36d627cd722402e687188b400333b https://github.com/galaxyproject/galaxy/commit/185856f6afd36d627cd722402e687... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-23 (Wed, 23 Nov 2016)

Changed paths: M config/galaxy.ini.sample

Log Message: ----------- Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo)

Commit: 5606d84f22e2bb21966c65ff37fd8c47013961c9 https://github.com/galaxyproject/galaxy/commit/5606d84f22e2bb21966c65ff37fd8... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-23 (Wed, 23 Nov 2016)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Rework cached dependencies to be more robust

to updates or changes in depedencies, folder structure and resolver configuration. Instead of hashing name, type and version of a dependency, hash the json representation of the dependencies returned by the dependency resolver, which include the path to the environment and the depedency type. This is only applied to resolvers whose cacheable attribute is set to True (conda-only, currently).

Commit: 66af4295cbb669389a68dcc19403798b84d0f2bc https://github.com/galaxyproject/galaxy/commit/66af4295cbb669389a68dcc194037... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-23 (Wed, 23 Nov 2016)

Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py

Log Message: ----------- Build dependency cache at install time

and only activate cached environments if they exist.

Commit: df93db40b118777cad6887386d7fc03df3acbf92 https://github.com/galaxyproject/galaxy/commit/df93db40b118777cad6887386d7fc... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-23 (Wed, 23 Nov 2016)

Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/tool_shed/galaxy_install/install_manager.py

Log Message: ----------- Only attempt to build cache once per install

and override __eq__ for ToolRequirement, to simplify checking if ToolRequirements are already installed/cached.

Commit: 21b859e555e6e199eece79cb1d718e7b17d827a1 https://github.com/galaxyproject/galaxy/commit/21b859e555e6e199eece79cb1d718... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-23 (Wed, 23 Nov 2016)

Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py

Log Message: ----------- Fix NameError

Commit: db93fd32859b9b1f326877833cb843edffd48d66 https://github.com/galaxyproject/galaxy/commit/db93fd32859b9b1f326877833cb84... Author: John Chilton jmchilton@gmail.com Date: 2016-11-23 (Wed, 23 Nov 2016)

Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py

Log Message: ----------- Merge pull request #3106 from mvdbeek/cached_dep_manager

Add cached dependency manager

Compare: https://github.com/galaxyproject/galaxy/compare/097300ea6219...db93fd32859b