November 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 5f04db: Fix typo in import error messages
by GitHub 20 Nov '18

20 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f04dbd996f4034aa9db45037c6c6e43518bcd1f https://github.com/galaxyproject/galaxy/commit/5f04dbd996f4034aa9db45037c6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Fix typo in import error messages Commit: c7bd5c794b3c0f6a34fe01c7928ca5dbf43284d5 https://github.com/galaxyproject/galaxy/commit/c7bd5c794b3c0f6a34fe01c7928c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Merge pull request #7033 from guerler/import_typos Fix typos in import error messages Compare: https://github.com/galaxyproject/galaxy/compare/fe671f67ec6b...c7bd5c794b3c **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.

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[galaxyproject/galaxy] 1b5fd3: Restore jquery style for text field autocomplete o...
by GitHub 20 Nov '18

20 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1b5fd373cb2f260c9f29afd2ed7722bbc0cd6299 https://github.com/galaxyproject/galaxy/commit/1b5fd373cb2f260c9f29afd2ed77… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M templates/js-app.mako Log Message: ----------- Restore jquery style for text field autocomplete options Commit: fe671f67ec6ba222115bb4c5c5a3705ca868b3a6 https://github.com/galaxyproject/galaxy/commit/fe671f67ec6ba222115bb4c5c5a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M templates/js-app.mako Log Message: ----------- Merge pull request #7027 from guerler/fix_text_options Use solid background for text field autocomplete options Compare: https://github.com/galaxyproject/galaxy/compare/6778fa47ed89...fe671f67ec6b **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.

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[galaxyproject/galaxy] 306b11: Pass a ``JobWrapper`` instead of a ``Job`` to ``st...
by GitHub 20 Nov '18

20 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 306b114191a1d326afcbdca68f489b015ba07660 https://github.com/galaxyproject/galaxy/commit/306b114191a1d326afcbdca68f48… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-17 (Sat, 17 Nov 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Pass a ``JobWrapper`` instead of a ``Job`` to ``stop_job()`` methods Commit: 0ddc5aeba1827833991cd782a9d806fa9ccd414e https://github.com/galaxyproject/galaxy/commit/0ddc5aeba1827833991cd782a9d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-17 (Sat, 17 Nov 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/model/__init__.py Log Message: ----------- Drop ``get_id()`` method Commit: 183d84e5dc8ce4530835852292f3d20318dc9980 https://github.com/galaxyproject/galaxy/commit/183d84e5dc8ce4530835852292f3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-17 (Sat, 17 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- 2 small simplifications in ``JobWrapper`` After commit eeb1dae5b71200ffe9f2056b2a7fd8ed560033c1, `JobWrapper.job_destination()` does not call `self._job_dataset_path_rewriter()` any more. Commit: 6778fa47ed899eefe1418139f43832f225760e0f https://github.com/galaxyproject/galaxy/commit/6778fa47ed899eefe1418139f438… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/model/__init__.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #7023 from nsoranzo/stop_job_wrapper Pass a ``JobWrapper`` instead of a ``Job`` to ``stop_job()`` methods Compare: https://github.com/galaxyproject/galaxy/compare/cd0b7a9347c8...6778fa47ed89 **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.

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[galaxyproject/galaxy] d35a07: Provide element_identifier attribute in DatsetColl...
by GitHub 20 Nov '18

20 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d35a07689891b5cff03976ca36e928cf10827594 https://github.com/galaxyproject/galaxy/commit/d35a07689891b5cff03976ca36e9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Provide element_identifier attribute in DatsetCollectionWrapper This allows accessing `$input1.element_identifier` for an `input1` of collection_type `list:pair`. Commit: cd0b7a9347c8cbe9df913cf65a6059157e6de3f0 https://github.com/galaxyproject/galaxy/commit/cd0b7a9347c8cbe9df913cf65a60… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/identifier_collection.xml Log Message: ----------- Merge pull request #7031 from mvdbeek/element_identifer_everywhere Provide element_identifier attribute in DatsetCollectionWrapper Compare: https://github.com/galaxyproject/galaxy/compare/d13792d64605...cd0b7a9347c8 **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.

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[galaxyproject/galaxy] eb3664: Only migrate distinct (input_step_id, input_name) ...
by GitHub 20 Nov '18

20 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb3664316ce9d7ab3f6d5d2c637b6901138c19a3 https://github.com/galaxyproject/galaxy/commit/eb3664316ce9d7ab3f6d5d2c637b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py Log Message: ----------- Only migrate distinct (input_step_id, input_name) pairs otherwise the UNIQUE constraint on the `workflow_step_input` table is violated. Follow-up on #6850. Reported by @mvdbeek. Commit: 797c2c5b270bb544773025e0d0d85855aba62d6b https://github.com/galaxyproject/galaxy/commit/797c2c5b270bb544773025e0d0d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py Log Message: ----------- Simplification of SQLAlchemy session handling Commit: d13792d64605bc3480eae5e877e933b1c111e28f https://github.com/galaxyproject/galaxy/commit/d13792d64605bc3480eae5e877e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py Log Message: ----------- Merge pull request #7029 from nsoranzo/followup_on_6850 Follow-up on #6850 Compare: https://github.com/galaxyproject/galaxy/compare/72b2781d4b22...d13792d64605 **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.

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[galaxyproject/galaxy] 55f523: A new runner for DRMAA (currently UNIVA)
by GitHub 19 Nov '18

19 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55f5235ab8b444a2ef20b03b9a03183cb5266ebb https://github.com/galaxyproject/galaxy/commit/55f5235ab8b444a2ef20b03b9a03… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-14 (Wed, 14 Nov 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/univa.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh Log Message: ----------- A new runner for DRMAA (currently UNIVA) Reimplementation of the DRMAA runner inspired by the SLURM runner. Currently tested only for the UNIVA grid engine (but I'm optimistic that it should work as well for other drmaa systems). This solves the problem that the current DRMAAJobRunner does not work when jobs are submitted as real user (because jobs that are started in a different drmaa session can not be accessed from the session that is open in galaxy): - this is done by resorting to command line tools qstat and qacct if the drmaa library can not be used to check the job status and to get run time information. - this has the additional advantage that if the drmaa library functions are not working (DRMAAJobRunner had implemented a repeated checking to handle this problem) the runner can still use the command line tools. Furthermore (in contrast to the original drmaa runner) the new one tests for run time and memory violations: - memory violations are determined by comparing the used and the requested memory - run time violations are determined by checking the signal that killed the job and by comparing the used and the requested run time Where the used memory and time are determined with drmaa.wait() or qacct Open (or better perspective): - adaptions to other grid engines. the current implementation (the command line calls and result parsing) might be specific for the Univa grid engine. to include other GEs one could determine the GE (+ version) and make the calls and result parsing depending on this. Implementation note: The changes in drmaa.py do not change the functionality at all, but only reorganize the code. In particular part of the function `check_watched_items` was put into a new function `check_watched_item` in order to make subclassing more convenient. Replaces #6931 (which replaced #4275), since I did mess up with git again (there were some duplicated commits). Commit: 72b2781d4b22cf1c6a312912ffc5333fe5db10b7 https://github.com/galaxyproject/galaxy/commit/72b2781d4b22cf1c6a312912ffc5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-19 (Mon, 19 Nov 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/univa.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh Log Message: ----------- Merge pull request #7004 from bernt-matthias/topic/univa3 A new runner for DRMAA (currently UNIVA) Compare: https://github.com/galaxyproject/galaxy/compare/f9685459a45f...72b2781d4b22 **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.

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[galaxyproject/galaxy] 67efd0: Track workflow step input definitions in our model...
by GitHub 16 Nov '18

16 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 67efd072ae98d6a34cbbc7f2270743524126bf8a https://github.com/galaxyproject/galaxy/commit/67efd072ae98d6a34cbbc7f22707… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py A lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/workflow_util.py M test/api/test_workflows.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Track workflow step input definitions in our model. We don't track workflow step inputs in any formal way in our model currently. This has resulted in some current hacks and prevents future enhancements. This commit splits WorkflowStepConnection into two models WorkflowStepInput and WorkflowStepConnection - normalizing the previous table workflow_step_connection on input step and input name. In terms of current hacks forced on it by restricting all of tool state to be confined to a big JSON blob in the database - we have problems distinguishing keys and values when walking tool state. As we store more and more JSON blobs inside of the giant tool state blob - the worse this problem gets. Take for instance checking for runtime parameters or the rules parameter values - these both use JSON blobs that aren't simple values, so it is hard to tell looking at the tool state blob in the database or the workflow export to tell what is a key or what is a value. Tracking state as normalized inputs with default values and explicit attributes runtime values should allow much more percise state definition and construction. This variant of the models would also potentially allow defining runtime values with non-tool default values (so default values defined for the workflow but still explicitly settable at runtime). The combinations of overriding defaults and defining runtime values were not representable before. In terms of future enhancements, there is a lot we cannot track with the current models - such as map/reduce options for collection operations (https://github.com/galaxyproject/galaxy/issues/4623#issuecomment-389544980) This should enable a lot of that. Obviously there are a lot of attributes defined here that are not yet utilized, but I'm using most (all?) of them downstream in the CWL branch. I'd rather populate this table fully realized and fill in the implementation around it as work continues to stream in from the CWL branch - to keep things simple and avoid extra database migrations. But I understand if this feels like speculative complexity we want to avoid despite the implementation being readily available for inspection downstream. Commit: 15c43e777b7c66614fd9d157ab2fcabb54d7f759 https://github.com/galaxyproject/galaxy/commit/15c43e777b7c66614fd9d157ab2f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Update lib/galaxy/model/mapping.py Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: 0a18ed62977b8a81932841361f7fa126f8dca2dc https://github.com/galaxyproject/galaxy/commit/0a18ed62977b8a81932841361f7f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py Log Message: ----------- Update lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: 00af4e21dee168fd6c54ac925414bcb95b8e7930 https://github.com/galaxyproject/galaxy/commit/00af4e21dee168fd6c54ac925414… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py Log Message: ----------- Update lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py Co-Authored-By: jmchilton <jmchilton(a)gmail.com> Commit: f2c17e589b734afedcb807d038d0f1b8caf27f52 https://github.com/galaxyproject/galaxy/commit/f2c17e589b734afedcb807d038d0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py Log Message: ----------- Preserve updated content in migration 145 downgrade Also add UNIQUE constraint to `("workflow_step_id", "name")` to the new `workflow_step_input` table. Commit: f9685459a45f2e2b3395077cbfa11e9a45245021 https://github.com/galaxyproject/galaxy/commit/f9685459a45f2e2b3395077cbfa1… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py A lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/workflow_util.py M test/api/test_workflows.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #6850 from jmchilton/workflows_track_step_inputs Track workflow step input definitions in our model. Compare: https://github.com/galaxyproject/galaxy/compare/7695569b50b7...f9685459a45f **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.

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[galaxyproject/galaxy] b8c97f: Added support for chaining dynamic destinations
by GitHub 16 Nov '18

16 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b8c97f108681e0e0963efc95a16af13be84642f9 https://github.com/galaxyproject/galaxy/commit/b8c97f108681e0e0963efc95a16a… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/jobs/mapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py Log Message: ----------- Added support for chaining dynamic destinations Commit: f46ab5a5dc21c1e8dd115ec3d9a37e0e3ee26a56 https://github.com/galaxyproject/galaxy/commit/f46ab5a5dc21c1e8dd115ec3d9a3… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/jobs/mapper.py Log Message: ----------- Fix debug logging Commit: f6c0e6ff9fdbf66a2af6d6538ad816274ecb93b3 https://github.com/galaxyproject/galaxy/commit/f6c0e6ff9fdbf66a2af6d6538ad8… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/jobs/mapper.py Log Message: ----------- Fixed issue with job_destination caching and added documentation Commit: c114ba4f43cb4e73fbff470f1283aed103e91fc2 https://github.com/galaxyproject/galaxy/commit/c114ba4f43cb4e73fbff470f1283… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/jobs/mapper.py M test/unit/jobs/test_mapper.py Log Message: ----------- Added test for cached_job_destination to prevent regression Commit: 766039adbd17490bf6e758311329b03917fefa18 https://github.com/galaxyproject/galaxy/commit/766039adbd17490bf6e758311329… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Added usage example of dynamic rule chaining Commit: ca7e2b9e68900e26a3be444f7269e21399176b10 https://github.com/galaxyproject/galaxy/commit/ca7e2b9e68900e26a3be444f7269… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: A test/integration/chained_dyndest_job_conf.xml A test/integration/chained_dyndest_rules/__init__.py A test/integration/chained_dyndest_rules/rules.py A test/integration/test_chained_dynamic_destinations.py Log Message: ----------- Added integration test for chained destinations Commit: 5ba1c24a1475c13f977fc2d1a6e02b5dc8158bb6 https://github.com/galaxyproject/galaxy/commit/5ba1c24a1475c13f977fc2d1a6e0… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M test/integration/chained_dyndest_job_conf.xml A test/integration/chained_dyndest_rules/module1/__init__.py A test/integration/chained_dyndest_rules/module1/rules.py A test/integration/chained_dyndest_rules/module2/__init__.py A test/integration/chained_dyndest_rules/module2/rules.py A test/integration/chained_dyndest_rules/module3/__init__.py A test/integration/chained_dyndest_rules/module3/rules.py R test/integration/chained_dyndest_rules/rules.py Log Message: ----------- Added integration test for rules_module overrides Commit: ae7869170762b08425c264b0d9777df0efd977ea https://github.com/galaxyproject/galaxy/commit/ae7869170762b08425c264b0d977… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M test/integration/test_chained_dynamic_destinations.py Log Message: ----------- Update test/integration/test_chained_dynamic_destinations.py Co-Authored-By: nuwang <nuwan.goonasekera(a)gmail.com> Commit: 7695569b50b7bb1ae249a248743612debd519f10 https://github.com/galaxyproject/galaxy/commit/7695569b50b7bb1ae249a2487436… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/mapper.py A test/integration/chained_dyndest_job_conf.xml A test/integration/chained_dyndest_rules/__init__.py A test/integration/chained_dyndest_rules/module1/__init__.py A test/integration/chained_dyndest_rules/module1/rules.py A test/integration/chained_dyndest_rules/module2/__init__.py A test/integration/chained_dyndest_rules/module2/rules.py A test/integration/chained_dyndest_rules/module3/__init__.py A test/integration/chained_dyndest_rules/module3/rules.py A test/integration/test_chained_dynamic_destinations.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rules/10_site.py Log Message: ----------- Merge pull request #7006 from nuwang/chained_dynamic_destinations Added support for chaining dynamic destinations Compare: https://github.com/galaxyproject/galaxy/compare/952847aad1eb...7695569b50b7 **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.

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[galaxyproject/galaxy] c06a14: Workflow test case, inputs as outputs.
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c06a142e04a9e034b3d991010fb910a775cabb21 https://github.com/galaxyproject/galaxy/commit/c06a142e04a9e034b3d991010fb9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Workflow test case, inputs as outputs. Commit: 952847aad1eb00f6150761127cce4456e2f880a5 https://github.com/galaxyproject/galaxy/commit/952847aad1eb00f6150761127cce… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-16 (Fri, 16 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #7016 from jmchilton/input_output_test_case Workflow test case - test marking inputs as outputs. Compare: https://github.com/galaxyproject/galaxy/compare/017ad2ccfbb2...952847aad1eb **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.

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[galaxyproject/galaxy] aa9fe3: Use cards for login forms
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa9fe3cb500603b7aaf5cc11b4875953d2c8e6ab https://github.com/galaxyproject/galaxy/commit/aa9fe3cb500603b7aaf5cc11b487… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M templates/user/login.mako Log Message: ----------- Use cards for login forms Commit: b697e0921182bacf249085138148b9e22cc1c8d7 https://github.com/galaxyproject/galaxy/commit/b697e0921182bacf249085138148… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M client/galaxy/style/scss/trackster.scss Log Message: ----------- Restore button defaults Commit: 1b4358653d7a7d5552a634fc34ffeba61b6b6228 https://github.com/galaxyproject/galaxy/commit/1b4358653d7a7d5552a634fc34ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M templates/user/reset_password.mako Log Message: ----------- Use card for password reset form Commit: 15e2c7ff8b31ce397a2c9fdfc98dcdcbdfe9d6d0 https://github.com/galaxyproject/galaxy/commit/15e2c7ff8b31ce397a2c9fdfc98d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M templates/user/register.mako Log Message: ----------- Use card for registration forms Commit: 017ad2ccfbb2434bd036b8ff1a36c25bfba827dd https://github.com/galaxyproject/galaxy/commit/017ad2ccfbb2434bd036b8ff1a36… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M client/galaxy/style/scss/trackster.scss M templates/user/login.mako M templates/user/register.mako M templates/user/reset_password.mako Log Message: ----------- Merge pull request #7017 from guerler/login_style Fix login and registration form appearance Compare: https://github.com/galaxyproject/galaxy/compare/7a10f5ce0ed8...017ad2ccfbb2 **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.

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