Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: ccb1e08000759184b2ebc4d26b8e88ebe9b4c9c4 https://github.com/galaxyproject/galaxy/commit/ccb1e08000759184b2ebc4d26b8e8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- In enqueue, always set an object_store_id if one isn't set. Tool actions other than the regular tool action (such as the upload ones) might not set an object store id even in the legacy mode. Commit: dc9128213fbf4fd1d479fc94ace5b2416a5face5 https://github.com/galaxyproject/galaxy/commit/dc9128213fbf4fd1d479fc94ace5b... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Fix traceback when starting under Python3 with ``galaxy.ini`` Update `paste` requirement to 3.0.4 to include: https://github.com/cdent/paste/pull/14 to fix the following traceback: ``` Starting server in PID 6792. Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/opt/galaxy/.venv3/lib/python3.5/site-packages/paste/httpserver.py", line 1358, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration galaxy.app DEBUG 2018-11-05 13:38:00,059 Shutting down ``` Commit: 9029b95e69795992ecf67f3ffdfa6384b52e1f3a https://github.com/galaxyproject/galaxy/commit/9029b95e69795992ecf67f3ffdfa6... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #6969 from jmchilton/ensure_better [18.09] In enqueue, always set an object_store_id if one isn't set. Commit: 6487d52d513b6351bd3e3e44e74e79c8f949919a https://github.com/galaxyproject/galaxy/commit/6487d52d513b6351bd3e3e44e74e7... Author: Dannon <dannon.baker@gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6978 from nsoranzo/release_18.09_paste [18.09] Fix traceback when starting under Python3 with ``galaxy.ini`` Commit: 0ecb4e7c595f7fb6cd6e648c4d770e1e97530424 https://github.com/galaxyproject/galaxy/commit/0ecb4e7c595f7fb6cd6e648c4d770... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- List tags as attribute of TestCollection Commit: bff5d51245f76bfc0bbe5b71237b3709d9ff7079 https://github.com/galaxyproject/galaxy/commit/bff5d51245f76bfc0bbe5b71237b3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use comma-separated instead of comma separated Commit: 5e098857e5dee703741e070e24a40235fb5deff2 https://github.com/galaxyproject/galaxy/commit/5e098857e5dee703741e070e24a40... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md Log Message: ----------- Display test collection input in documentation Commit: 5e1fb9a7a2935fc3a3e599b6111157c91fe7b345 https://github.com/galaxyproject/galaxy/commit/5e1fb9a7a2935fc3a3e599b611115... Author: John Chilton <jmchilton@gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6983 from mvdbeek/schema_amamdment_tags_in_collection [18.09] List tags as attribute of TestCollection Commit: 51498fc994f10d7c7bb71948b265f3c93c6ca7bf https://github.com/galaxyproject/galaxy/commit/51498fc994f10d7c7bb71948b265f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M doc/schema_template.md M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge branch 'release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/fefa132cd741...51498fc994f1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.