Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74d8faac9f07407ac9df344a78c9ecb06c178f93 https://github.com/galaxyproject/galaxy/commit/74d8faac9f07407ac9df344a78c9e... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js 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/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Change 'History Actions' to 'Current History' in history options menu. as it was before 1cc57b1eb2c295dbd68837c864740b6ff079b83d. Commit: ec08ec60bb4dadaf6f8759f9dce79f764f26c909 https://github.com/galaxyproject/galaxy/commit/ec08ec60bb4dadaf6f8759f9dce79... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js 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/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3205 from blankenberg/history-current-options-name_16.10 [16.10] Change 'History Actions' to 'Current History' in history options menu. Commit: a9dab631fb00252ac122ea297262e89f63887019 https://github.com/galaxyproject/galaxy/commit/a9dab631fb00252ac122ea297262e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-section.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-section.js Log Message: ----------- Preserve custom event handler for form inputs Commit: 0b2d0c1746c9b7d7cc5781fedc5c6a02af3bdfdb https://github.com/galaxyproject/galaxy/commit/0b2d0c1746c9b7d7cc5781fedc5c6... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-section.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-section.js Log Message: ----------- Merge pull request #3210 from guerler/fix_output_label_handler [16.10] Preserve custom event handler for form inputs Commit: 9a2bae7381b1ee8e2411681a76d75767b05ceffe https://github.com/galaxyproject/galaxy/commit/9a2bae7381b1ee8e2411681a76d75... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- simplify the UI of deps installation by hiding the details under toggle button Commit: 068ee6bd0ceb942ec67e634a7e6e434314cbe7fe https://github.com/galaxyproject/galaxy/commit/068ee6bd0ceb942ec67e634a7e6e4... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py Log Message: ----------- fix install repo test Commit: 706bc3fbb118087cc057e6559e0262a6aca31127 https://github.com/galaxyproject/galaxy/commit/706bc3fbb118087cc057e6559e026... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py Log Message: ----------- fix test and hide shed_conf select udner details Commit: 73d010efa4236ed8ef0e46bb10d5e39233ae2d6b https://github.com/galaxyproject/galaxy/commit/73d010efa4236ed8ef0e46bb10d5e... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- fix another test Commit: 4b794729b0cfd347d189a9a1e62273ab1788bc3e https://github.com/galaxyproject/galaxy/commit/4b794729b0cfd347d189a9a1e6227... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- fix a bug that renders conda dependency selection everytime Commit: 94edc94b73e047612ae51ca2e075f17ac8e238bb https://github.com/galaxyproject/galaxy/commit/94edc94b73e047612ae51ca2e075f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 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: 0a9b6d8755dee530232ab893a3bad199407aa0bc https://github.com/galaxyproject/galaxy/commit/0a9b6d8755dee530232ab893a3bad... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo) Commit: 2b1765751b29008aecbd782f28269ac4e63db239 https://github.com/galaxyproject/galaxy/commit/2b1765751b29008aecbd782f28269... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 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: f919a98601252ab8f87bffff6e449105e770aadf https://github.com/galaxyproject/galaxy/commit/f919a98601252ab8f87bffff6e449... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 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: 82f30e7645156b5f35c2b4cd77314e6275663979 https://github.com/galaxyproject/galaxy/commit/82f30e7645156b5f35c2b4cd77314... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 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: 64bc9241ed785d4d552c5fac21cd412558c54567 https://github.com/galaxyproject/galaxy/commit/64bc9241ed785d4d552c5fac21cd4... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix NameError Commit: cf769dd09deb73624b22628208fa103cc4f27150 https://github.com/galaxyproject/galaxy/commit/cf769dd09deb73624b22628208fa1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 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: cc7cd47ef54a09efbf8272d1e024f6f2ac92594b https://github.com/galaxyproject/galaxy/commit/cc7cd47ef54a09efbf8272d1e024f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Add integration test-case for install tool dependency API endpoint Commit: f10fd793a68ed9413bec708daa48cef65769d09f https://github.com/galaxyproject/galaxy/commit/f10fd793a68ed9413bec708daa48c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml Log Message: ----------- Install the correct converter dependency Commit: 045a2f0d471f7b4186aff625f3cea9abfa549fa2 https://github.com/galaxyproject/galaxy/commit/045a2f0d471f7b4186aff625f3cea... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 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: 16b49d9140edbf116f83b51b957cd61c4f2d91df https://github.com/galaxyproject/galaxy/commit/16b49d9140edbf116f83b51b957cd... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 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: 1efd4d4b3b99ec40071aa4d6fb7cf4030c51e2e0 https://github.com/galaxyproject/galaxy/commit/1efd4d4b3b99ec40071aa4d6fb7cf... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-11-29 (Tue, 29 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: 2a4ccac4039342c98d71bc72177aa951db6c4ba1 https://github.com/galaxyproject/galaxy/commit/2a4ccac4039342c98d71bc72177aa... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-29 (Tue, 29 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: e3f8b724648cee51636502959096adba88045e14 https://github.com/galaxyproject/galaxy/commit/e3f8b724648cee51636502959096a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Merge pull request #3226 from martenson/16-10-install-ux [16.10] admin installation ux Commit: d6f0e6b37c318a0202e0e266828e6325100cab19 https://github.com/galaxyproject/galaxy/commit/d6f0e6b37c318a0202e0e266828e6... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py 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/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.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 lib/tool_shed/galaxy_install/install_manager.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3227 from mvdbeek/cached_deps_16.10 [16.10] Backport #3106 and #3222: Cached conda environments and API to manage them Commit: a26568bdfaefc5748ff3b2385fa9424ece6c652c https://github.com/galaxyproject/galaxy/commit/a26568bdfaefc5748ff3b2385fa94... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and flake8-import-order Do not pin when forward-merging to dev branch! Commit: 888a8f91537e22dcbdea174a65eaecbced9ea8a8 https://github.com/galaxyproject/galaxy/commit/888a8f91537e22dcbdea174a65eae... Author: John Chilton <jmchilton@gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3232 from nsoranzo/release_16.10_pin_flake8 [16.10] Pin flake8 and flake8-import-order Commit: 2d510fae981f0255f04b21272f99e995f0a16f0b https://github.com/galaxyproject/galaxy/commit/2d510fae981f0255f04b21272f99e... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/user/user-preferences.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-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/maps/mvc/form/form-section.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js.map static/scripts/mvc/form/form-section.js Compare: https://github.com/galaxyproject/galaxy/compare/1bbab2d89d2c...2d510fae981f