Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 40a95a300326bddeb0e78add288a47f4f23c087c https://github.com/galaxyproject/galaxy/commit/40a95a300326bddeb0e78add288a4... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-27 (Sun, 27 Nov 2016)

Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py

Log Message: ----------- Add API to install resolver tool dependencies

and to build a tool dependency cache (if activated in galaxy.ini).

An example to install dependencies for the twobit converter: ``` import bioblend.galaxy url = 'http://localhost:8080/' api_key = 'admin_api_key' tool_id = 'CONVERTER_fasta_to_2bit' endpoint = "api/tools/%s/install_dependencies" % tool_id gi = bioblend.galaxy.GalaxyInstance(url, api_key) gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id}) ``` If `use_cached_dependency_manager` is activated in the galaxy.ini, a cached environment can be built like this: ``` endpoint = "api/tools/%s/build_dependency_cache" % tool_id gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id}) ```

Commit: e905b8baeb9081400ad775bcc20c2956808a11fd https://github.com/galaxyproject/galaxy/commit/e905b8baeb9081400ad775bcc20c2... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-27 (Sun, 27 Nov 2016)

Changed paths: M test/integration/test_resolvers.py

Log Message: ----------- Add integration test-case for install tool dependency API endpoint

Commit: 3e48f3792bc10c081a8079cfa3d773531d6dad15 https://github.com/galaxyproject/galaxy/commit/3e48f3792bc10c081a8079cfa3d77... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-27 (Sun, 27 Nov 2016)

Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml

Log Message: ----------- Install the correct converter dependency

Commit: 8ff7ffa063c491b886bbeed1e1eb2e69fb6f3e68 https://github.com/galaxyproject/galaxy/commit/8ff7ffa063c491b886bbeed1e1eb2... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-27 (Sun, 27 Nov 2016)

Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py

Log Message: ----------- Add `force_rebuild` param to build_dependency_cache

This will remove a pre-existing cached dependency directory.

Commit: 3ebbb37c4dc09648ee08877eeb87a1db90a75d35 https://github.com/galaxyproject/galaxy/commit/3ebbb37c4dc09648ee08877eeb87a... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-27 (Sun, 27 Nov 2016)

Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py

Log Message: ----------- Add dependency_resolvers/clean endpoint

Commit: 23c6b1c6ff6b810fed69c05eec74166cd2d8fc5f https://github.com/galaxyproject/galaxy/commit/23c6b1c6ff6b810fed69c05eec741... Author: Bjoern Gruening bjoern.gruening@gmail.com Date: 2016-11-27 (Sun, 27 Nov 2016)

Changed paths: M lib/galaxy/tools/deps/conda_util.py

Log Message: ----------- add a conda clean function to remove downloaded tarballs after installation

Commit: 00ca0a600a083bf05e2c8f90610851972e7e94ea https://github.com/galaxyproject/galaxy/commit/00ca0a600a083bf05e2c8f9061085... Author: mvdbeek m.vandenbeek@gmail.com Date: 2016-11-28 (Mon, 28 Nov 2016)

Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py

Log Message: ----------- Connect `clean` endpoint properly and add `-y` to exec_clean

Commit: fd0a52a9a9aeba2e9ac5b555992c481a562b9162 https://github.com/galaxyproject/galaxy/commit/fd0a52a9a9aeba2e9ac5b555992c4... Author: John Chilton jmchilton@gmail.com Date: 2016-11-28 (Mon, 28 Nov 2016)

Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml 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/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py

Log Message: ----------- Merge pull request #3222 from mvdbeek/api_cache_env

Add API to install resolver tool dependencies

Compare: https://github.com/galaxyproject/galaxy/compare/c8ea393ccb13...fd0a52a9a9ae