Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 92948b5b0fc062ce904c5987c1d48d3831730a9a https://github.com/galaxyproject/galaxy/commit/92948b5b0fc062ce904c5987c1d48... Author: guerler <aysam.guerler@gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Overload select wrapper`s concat function Commit: e4a35f943b42401c92646d8f6b7b1c1fd515a9c1 https://github.com/galaxyproject/galaxy/commit/e4a35f943b42401c92646d8f6b7b1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Paste handles encoding automatically when thrown unicode, but uwsgi does not. This was resulting in unencoded (unicode) workflow drawings (svg) not appearing at all when the gen_image was invoked. Also took the opportunity to add a correct header for a standalone svg document. Commit: e37850386ecc8122abeb6695ffc76eb513f34516 https://github.com/galaxyproject/galaxy/commit/e37850386ecc8122abeb6695ffc76... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M static/maps/mvc/collection/collection-li.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/collection/collection-li.js Log Message: ----------- UI, HDCAs: render element_count when available - Adds a change event for element_count that renders the subtitle - Subtitle now renders the count or nothing if not available Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: 6b64af72deafee0382cb5b9c83ed39a3fa42e1c9 https://github.com/galaxyproject/galaxy/commit/6b64af72deafee0382cb5b9c83ed3... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- UI, history: doc updates Conflicts: client/galaxy/scripts/mvc/history/history-contents.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: 654748763af10aa87d3afe9fdf9ea686520ede7e https://github.com/galaxyproject/galaxy/commit/654748763af10aa87d3afe9fdf9ea... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.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/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: implement list:list Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/history/history-contents.js Commit: d550024d56c063bb78e4855395cfbf0cc440fe08 https://github.com/galaxyproject/galaxy/commit/d550024d56c063bb78e4855395cfb... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: more feedback on bad collection type Conflicts: static/maps/mvc/history/history-contents.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 static/scripts/bundled/login.bundled.js.map static/scripts/mvc/history/history-contents.js Commit: 0d49b06bac4a5c4a4b94e48517d1c0f5de713d42 https://github.com/galaxyproject/galaxy/commit/0d49b06bac4a5c4a4b94e48517d1c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M static/maps/mvc/history/history-contents.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- repack Commit: 132bd4dd57e084ec8e743e1360e7d2a0faa29ac6 https://github.com/galaxyproject/galaxy/commit/132bd4dd57e084ec8e743e1360e7d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.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/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- Merge branch 'backport_2613' into release_16.04 (and rebuild client) Commit: 68a64182c14af9f4cc10915c466177292d24ebfc https://github.com/galaxyproject/galaxy/commit/68a64182c14af9f4cc10915c46617... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #2628 from dannon/workflow_svg_uwsgi_fix [16.04] Workflow SVG generation fix Commit: 1de7beca98d0bc8b11b9dca46a4984ac1cee9428 https://github.com/galaxyproject/galaxy/commit/1de7beca98d0bc8b11b9dca46a498... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #2623 from guerler/fix_select_value_concat [16.04] Overload select wrapper`s concat function Commit: 4a831033ed820e3f1220d9d326f8bd8079c390f9 https://github.com/galaxyproject/galaxy/commit/4a831033ed820e3f1220d9d326f8b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Generate metadata in separate conda environment Galaxy supports generating metadata in a separate command (enable beta_tool_command_isolation). This command has its own dependency resolution, that may interfere with thedependency resolution of the actual tool, if the same environment is being used. With this PR we create a new environment when resolving metadata dependencies with conda, that will be active only for metadata generation. Commit: 28da4b6371b23c69d15e7fc59473d4bde5639fde https://github.com/galaxyproject/galaxy/commit/28da4b6371b23c69d15e7fc59473d... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix whitespace and comma use Commit: f8cf81d73693e5f075b6c9e612244221bbd6e5bb https://github.com/galaxyproject/galaxy/commit/f8cf81d73693e5f075b6c9e612244... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore. Commit: f0024d64e15815dcb6c2ac027ed5fb2977651e64 https://github.com/galaxyproject/galaxy/commit/f0024d64e15815dcb6c2ac027ed5f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py Log Message: ----------- Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it) Commit: 8f978b8957f0cbc7e5d78ca3f3bce9e87e6e8f76 https://github.com/galaxyproject/galaxy/commit/8f978b8957f0cbc7e5d78ca3f3bce... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py Log Message: ----------- Merge pull request #2662 from jmchilton/backport_2253 [16.04] Backport #2253 as requested by Eagle Eyes Commit: 5d8d932425c879177c40a008a5a2ef3e45020b73 https://github.com/galaxyproject/galaxy/commit/5d8d932425c879177c40a008a5a2e... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Add hg38 to main for ucsc_build_sites.txt.sample (cherry picked from commit 04b7d11f053e66b14232440e6ff534a62ff26666) Commit: e4ca3bf80fcab185e8ea3502926563707b047236 https://github.com/galaxyproject/galaxy/commit/e4ca3bf80fcab185e8ea350292656... Author: Enis Afgan <afgane@gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04 [16.04] Add hg38 to main for ucsc_build_sites.txt.sample Commit: b39f2143fac4f2be29477d4b1c5542bfe7dd0946 https://github.com/galaxyproject/galaxy/commit/b39f2143fac4f2be29477d4b1c554... Author: John Chilton <jmchilton@gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix to mount job directory in Docker for #1688. The default for this was including GALAXY_ROOT so in testing (and many deployments) the job directory would have been picked up anyway because it is in `database/` but if job directory was outside of `$GALAXY_ROOT/database/` one needed to add it to the volumes mounted by Docker. This fix mounts just that directory - so no need for instance to mount all job directories which one could have done. Commit: a7664f00f92a97258050d580aef1b6e439cc2f6d https://github.com/galaxyproject/galaxy/commit/a7664f00f92a97258050d580aef1b... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2745 from jmchilton/16.04_fix_docker_job_directory_default [16.04] Fix to mount job directory in Docker for #1688. Commit: fb76aa0a938a2498d3206e6039bc1d9906e6c2ce https://github.com/galaxyproject/galaxy/commit/fb76aa0a938a2498d3206e6039bc1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/wrappers.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.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/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js M test/base/driver_util.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/a5b836e9eeea...fb76aa0a938a