- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] 880605: change join two dataset output format to auto
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 880605f17d9bd337789b783840c0fb4d35ddbe9d https://github.com/galaxyproject/galaxy/commit/880605f17d9bd337789b783840c0… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M tools/filters/joiner.xml Log Message: ----------- change join two dataset output format to auto Commit: d2f01b3d000d68378e456aa46e5ec32a9fea506c https://github.com/galaxyproject/galaxy/commit/d2f01b3d000d68378e456aa46e5e… Author: Qiang Gu <36086881+qiagu(a)users.noreply.github.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M tools/filters/joiner.xml Log Message: ----------- Update joiner.xml Commit: aaf49d6d067e84dbf31b52a45dbe7d7156dd59f3 https://github.com/galaxyproject/galaxy/commit/aaf49d6d067e84dbf31b52a45dbe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M tools/filters/joiner.xml Log Message: ----------- Update tools/filters/joiner.xml Co-Authored-By: qiagu <36086881+qiagu(a)users.noreply.github.com> Commit: cf86049c0c46908fa6fd87c7b1221e86b1faf13f https://github.com/galaxyproject/galaxy/commit/cf86049c0c46908fa6fd87c7b122… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M tools/filters/joiner.xml Log Message: ----------- update help of joiner two datasets tool Commit: 7a10f5ce0ed809ba1ab836f6a295c4fca9a637de https://github.com/galaxyproject/galaxy/commit/7a10f5ce0ed809ba1ab836f6a295… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M tools/filters/joiner.xml Log Message: ----------- Merge pull request #6998 from qiagu/join1 Change join two dataset output format to tabular Compare: https://github.com/galaxyproject/galaxy/compare/265a43507ebd...7a10f5ce0ed8 **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] 649d8b: Added support for overriding the rules module per ...
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 649d8bad5280174c2f9a74bd847a44ba7158ec3f https://github.com/galaxyproject/galaxy/commit/649d8bad5280174c2f9a74bd847a… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/jobs/mapper.py Log Message: ----------- Added support for overriding the rules module per destination Commit: 65979e473c5623a5116819bd93c182744117e6f0 https://github.com/galaxyproject/galaxy/commit/65979e473c5623a5116819bd93c1… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M test/unit/jobs/test_mapper.py A test/unit/jobs/test_rules_override/10_rule.py A test/unit/jobs/test_rules_override/__init__.py Log Message: ----------- Added test for rules module overriding Commit: 33b7f0f9d1e105dfbcbdab0a92081a9302cfe7eb https://github.com/galaxyproject/galaxy/commit/33b7f0f9d1e105dfbcbdab0a9208… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/jobs/mapper.py Log Message: ----------- Refactor to use importlib Commit: 4b5312fe80fe4d8bc0a429229d84366b630d8eac https://github.com/galaxyproject/galaxy/commit/4b5312fe80fe4d8bc0a429229d84… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Updated watchers to reload rule module overrides Commit: bf1f2fe0ab5248acd86d646f1c80314561c0cdc2 https://github.com/galaxyproject/galaxy/commit/bf1f2fe0ab5248acd86d646f1c80… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/tools/lint.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/submodules.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/jobs/test_mapper.py Log Message: ----------- Refactor submodule imports Commit: 265a43507ebda1bac9bc5dbe2ac601912bef66d8 https://github.com/galaxyproject/galaxy/commit/265a43507ebda1bac9bc5dbe2ac6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/lint.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/submodules.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/jobs/test_mapper.py A test/unit/jobs/test_rules_override/10_rule.py A test/unit/jobs/test_rules_override/__init__.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #6993 from nuwang/allow_rules_module_override Allow rules module override and refactor submodule imports Compare: https://github.com/galaxyproject/galaxy/compare/17299356f011...265a43507ebd **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] 5385ca: Fix handling of forgotten LSF jobs in cli
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5385ca0473be64f4cde24fef07b5a38f47e9444f https://github.com/galaxyproject/galaxy/commit/5385ca0473be64f4cde24fef07b5… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Fix handling of forgotten LSF jobs in cli Previous case assumed that "is not found" was part of the STDOUT when in fact is in the STDERR (and STDOUT is empty). Commit: bfa7b200526bccf4dc0ffe888972ffe879f688bc https://github.com/galaxyproject/galaxy/commit/bfa7b200526bccf4dc0ffe888972… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Add log warning for missing LSF jobs. Co-Authored-By: pcm32 <pcm32(a)users.noreply.github.com> Commit: 17299356f011b80dcf575399be5d6803a1f31cc7 https://github.com/galaxyproject/galaxy/commit/17299356f011b80dcf575399be5d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/job/lsf.py Log Message: ----------- Merge pull request #7007 from pcm32/patch-2 Fix handling of forgotten LSF jobs in cli Compare: https://github.com/galaxyproject/galaxy/compare/eaacc5bc9f35...17299356f011 **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/usegalaxy-playbook] 6ab7c3: Set downtime banner
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6ab7c39a5db5d8a6dcedf94e2dfad1f2bcd37526 https://github.com/galaxyproject/usegalaxy-playbook/commit/6ab7c39a5db5d8a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Set downtime banner **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] 2299e0: Add StoredWorkflow.show_in_tool_panel function
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 2299e06a6937328f36485a8baa136c1138461144 https://github.com/galaxyproject/galaxy/commit/2299e06a6937328f36485a8baa13… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add StoredWorkflow.show_in_tool_panel function This is more DRY and fixes https://github.com/galaxyproject/galaxy/issues/6889#issuecomment-438991091. The bug itself was due to comparing the id of a StoredWorkflowUserShareAssociation instead of StoredWorkflow when checking if a stored workflow should be in the tool panel. Commit: b5ce8d0dcf5affd462e33902126d4dd5c5921be6 https://github.com/galaxyproject/galaxy/commit/b5ce8d0dcf5affd462e33902126d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7014 from mvdbeek/fix_inability_to_remove_workflow_from_panel [18.01] Fix display_in_tool_panel status for shared workflows Compare: https://github.com/galaxyproject/galaxy/compare/baa992d21703...b5ce8d0dcf5a **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] 4760a0: Fix recursion issue in gff_filter_by_feature_count
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 4760a0ac0f48b106f9a1cee348deeccc223eb64a https://github.com/galaxyproject/galaxy/commit/4760a0ac0f48b106f9a1cee348de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix recursion issue in gff_filter_by_feature_count Commit: 45e475e19aa1988db2461c1d7fdf6135c02294d0 https://github.com/galaxyproject/galaxy/commit/45e475e19aa1988db2461c1d7fdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #6986 from nsoranzo/release_18.05_backport_2d36e8955e020958334088d6ba5853c1027d8b75 [18.05] Backport commit 2d36e8955e020958334088d6ba5853c1027d8b75 Commit: f85afad9655b970f3af895a8dfafc0b8e301c705 https://github.com/galaxyproject/galaxy/commit/f85afad9655b970f3af895a8dfaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-08 (Thu, 08 Nov 2018) Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: fbd2284e5d355e8698360b5744538eb5f0a693ab https://github.com/galaxyproject/galaxy/commit/fbd2284e5d355e8698360b574453… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Fix PID file handling for gunicorn gunicorn uses `--pid`, not `--pid-file`. Commit: a1277b0e43b24594e25cc612ad844b501c7fb39b https://github.com/galaxyproject/galaxy/commit/a1277b0e43b24594e25cc612ad84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7013 from nsoranzo/release_18.09_fix_gunicorn_pid [18.09] Fix PID file handling for gunicorn Commit: 1ae8eb577db9d786f69b89226019a3ad8b437e58 https://github.com/galaxyproject/galaxy/commit/1ae8eb577db9d786f69b89226019… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge branch 'release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/51498fc994f1...1ae8eb577db9 **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] fbd228: Fix PID file handling for gunicorn
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fbd2284e5d355e8698360b5744538eb5f0a693ab https://github.com/galaxyproject/galaxy/commit/fbd2284e5d355e8698360b574453… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Fix PID file handling for gunicorn gunicorn uses `--pid`, not `--pid-file`. Commit: a1277b0e43b24594e25cc612ad844b501c7fb39b https://github.com/galaxyproject/galaxy/commit/a1277b0e43b24594e25cc612ad84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7013 from nsoranzo/release_18.09_fix_gunicorn_pid [18.09] Fix PID file handling for gunicorn Commit: eaacc5bc9f351b8a01281ffa3462e1c653db3826 https://github.com/galaxyproject/galaxy/commit/eaacc5bc9f351b8a01281ffa3462… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d88f2b63daa9...eaacc5bc9f35 **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.

1 0

[galaxyproject/galaxy] fbd228: Fix PID file handling for gunicorn
by GitHub 15 Nov '18

15 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: fbd2284e5d355e8698360b5744538eb5f0a693ab https://github.com/galaxyproject/galaxy/commit/fbd2284e5d355e8698360b574453… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Fix PID file handling for gunicorn gunicorn uses `--pid`, not `--pid-file`. Commit: a1277b0e43b24594e25cc612ad844b501c7fb39b https://github.com/galaxyproject/galaxy/commit/a1277b0e43b24594e25cc612ad84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-15 (Thu, 15 Nov 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #7013 from nsoranzo/release_18.09_fix_gunicorn_pid [18.09] Fix PID file handling for gunicorn Compare: https://github.com/galaxyproject/galaxy/compare/f85afad9655b...a1277b0e43b2 **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] ab75fe: Update pysam to v0.15.1
by GitHub 13 Nov '18

13 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab75fe8a37c4aaef2724bb1746f0fb7bb32c6fab https://github.com/galaxyproject/galaxy/commit/ab75fe8a37c4aaef2724bb1746f0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-12 (Mon, 12 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update pysam to v0.15.1 For Python 3.7 compatibility. Reported by @wm75. Commit: a53629ebae992e685020676f72cbcb55c954b677 https://github.com/galaxyproject/galaxy/commit/a53629ebae992e685020676f72cb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Update virtualenv installation to v16.1.0 which bundles `wheel` 0.32.2. The old virtualenv 13.1.2 included wheel 0.24.0, where tagging is broken for Python >=3.5, producing tracebacks like: ``` Traceback (most recent call last): File "<string>", line 1, in <module> File "/tmp/pip-install-c53eutpg/uwsgi/setup.py", line 138, in <module> 'Programming Language :: Python :: 3.6', File "/tmp/wheel_venv/lib/python3.7/site-packages/setuptools/__init__.py", line 143, in setup return distutils.core.setup(**attrs) File "/usr/lib/python3.7/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 213, in run archive_basename = self.get_archive_basename() File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 161, in get_archive_basename impl_tag, abi_tag, plat_tag = self.get_tag() File "/tmp/wheel_venv/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 155, in get_tag assert tag == supported_tags[0] AssertionError ``` This was fixed in wheel 0.25.0. Reported by @wm75. Also update `urlretrieve` import for Python 3. Commit: d88f2b63daa91f1fce1ca161f9a9192ce20a5cd5 https://github.com/galaxyproject/galaxy/commit/d88f2b63daa91f1fce1ca161f9a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #7008 from nsoranzo/python3.7 Fixes for Python 3.7 Compare: https://github.com/galaxyproject/galaxy/compare/0395fcabf083...d88f2b63daa9 **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] 688bf3: Fix getAppRoot in layout/data.js
by GitHub 13 Nov '18

13 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 688bf3d524f7495afaf9c202a3601101baffb760 https://github.com/galaxyproject/galaxy/commit/688bf3d524f7495afaf9c202a360… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Fix getAppRoot in layout/data.js Commit: 0395fcabf083525beb1155c631a27046fa02d3a6 https://github.com/galaxyproject/galaxy/commit/0395fcabf083525beb1155c631a2… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Merge pull request #7009 from dannon/app_singleton_cleaned Fix getAppRoot in layout/data.js Compare: https://github.com/galaxyproject/galaxy/compare/4ea20bc95915...0395fcabf083 **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] a4ce32: added singleton functions
by GitHub 13 Nov '18

13 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a4ce326d8e8bbf812f5573bfe6c14fb566b2be1a https://github.com/galaxyproject/galaxy/commit/a4ce326d8e8bbf812f5573bfe6c1… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-10 (Sat, 10 Nov 2018) Changed paths: A client/galaxy/scripts/app/galaxy.js A client/galaxy/scripts/app/index.js A client/galaxy/scripts/app/monitor.js A client/galaxy/scripts/app/singleton.js R client/galaxy/scripts/galaxy.js R client/galaxy/scripts/galaxy.monitor.js M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/utils/serverPath.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/webpack.config.js Log Message: ----------- added singleton functions Commit: 4ed27cf13145a77b4f8f1bcd57acbf1bb867886a https://github.com/galaxyproject/galaxy/commit/4ed27cf13145a77b4f8f1bcd57ac… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-10 (Sat, 10 Nov 2018) Changed paths: M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/test-data/bootstrapped.js M client/galaxy/scripts/qunit/test-data/fakeserver.js M client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/json/datatypes.json A client/galaxy/scripts/qunit/test-data/json/datatypes.mapping.json A client/galaxy/scripts/qunit/test-data/json/tools.test.build.json M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js M client/galaxy/scripts/qunit/tests/graph_tests.js M client/galaxy/scripts/qunit/tests/hda_base_tests.js M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js M client/galaxy/scripts/qunit/tests/job_dag_tests.js A client/galaxy/scripts/qunit/tests/jquery_plugin_tests.js M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/metrics_logger_tests.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js M client/galaxy/scripts/qunit/tests/utils_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js Log Message: ----------- Added qunit tests Commit: d4ab893441a5dd8f7a82df902323a5940e1698d7 https://github.com/galaxyproject/galaxy/commit/d4ab893441a5dd8f7a82df902323… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-10 (Sat, 10 Nov 2018) Changed paths: M templates/base.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Modified python templates Commit: 969263e94805ff1c2b4568c3bf127d4183515cb4 https://github.com/galaxyproject/galaxy/commit/969263e94805ff1c2b4568c3bf12… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-10 (Sat, 10 Nov 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js Log Message: ----------- Updated entry points to use singleton Commit: 964875f58a39c36032b7d958d5f3739643ea0dc2 https://github.com/galaxyproject/galaxy/commit/964875f58a39c36032b7d958d5f3… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-10 (Sat, 10 Nov 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.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/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/toolshed/groups/group-model.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/karma/karma.config.qunit.js M client/karma/webpack.config.unittest.js Log Message: ----------- Removed global references to Galaxy Commit: 020bbe92763e98c39c9d345a661dcf5475218d86 https://github.com/galaxyproject/galaxy/commit/020bbe92763e98c39c9d345a661d… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-12 (Mon, 12 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M lib/galaxy/datatypes/sequence.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M scripts/drmaa_external_runner.py M test/api/test_workflows.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merged dev, noted unused variables in workflow-node.js but harmless Commit: 57abad3fa603fdb8325d1eeea61709959eb1dcdb https://github.com/galaxyproject/galaxy/commit/57abad3fa603fdb8325d1eeea617… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-12 (Mon, 12 Nov 2018) Changed paths: M client/galaxy/scripts/app/singleton.js Log Message: ----------- Replaced string-based type comparison with instanceof, fixed production-only build issue where constructor names become uglified Commit: bdf5c06f04ab4743a5e18872446d4af96f9877db https://github.com/galaxyproject/galaxy/commit/bdf5c06f04ab4743a5e18872446d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/app/index.js M client/galaxy/scripts/app/monitor.js M client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/test-data/bootstrapped.js M client/galaxy/scripts/qunit/test-data/fakeserver.js M client/galaxy/scripts/qunit/test-data/job-dag-1.js M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js M client/galaxy/scripts/qunit/tests/metrics_logger_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Client format. Commit: c2ac98b9bb48d938fbebc5c70ce563fcb4717ad4 https://github.com/galaxyproject/galaxy/commit/c2ac98b9bb48d938fbebc5c70ce5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Update layout/data to use getGalaxyInstance/etc Commit: 4ea20bc95915c5a1f4046f31d3b50e11516540d0 https://github.com/galaxyproject/galaxy/commit/4ea20bc95915c5a1f4046f31d3b5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/app/galaxy.js A client/galaxy/scripts/app/index.js A client/galaxy/scripts/app/monitor.js A client/galaxy/scripts/app/singleton.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataManager/DataManager.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJob.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerJobs.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerRouter.vue M client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTypes.vue R client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.monitor.js M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.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/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/test-data/bootstrapped.js M client/galaxy/scripts/qunit/test-data/fakeserver.js M client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/json/datatypes.json A client/galaxy/scripts/qunit/test-data/json/datatypes.mapping.json A client/galaxy/scripts/qunit/test-data/json/tools.test.build.json M client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js M client/galaxy/scripts/qunit/tests/graph_tests.js M client/galaxy/scripts/qunit/tests/hda_base_tests.js M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js M client/galaxy/scripts/qunit/tests/job_dag_tests.js A client/galaxy/scripts/qunit/tests/jquery_plugin_tests.js M client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/metrics_logger_tests.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js M client/galaxy/scripts/qunit/tests/utils_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/scripts/toolshed/groups/group-model.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/installMonitor.js M client/galaxy/scripts/utils/serverPath.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/karma/karma.config.qunit.js M client/karma/webpack.config.unittest.js M client/webpack.config.js M templates/base.mako M templates/galaxy_client_app.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #7005 from Nerdinacan/app_singleton_cleaned Replace global Galaxy references with galaxy singleton accessor/setter Compare: https://github.com/galaxyproject/galaxy/compare/be76d9f8017e...4ea20bc95915 **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.

1 0

[galaxyproject/usegalaxy-playbook] a7d0ba: Installed latest GEMINI tools.
by GitHub 13 Nov '18

13 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a7d0bab3ca7abf4eadb8e7ad5342961560f73fc6 https://github.com/galaxyproject/usegalaxy-playbook/commit/a7d0bab3ca7abf4e… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-11-13 (Tue, 13 Nov 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed latest GEMINI tools. **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.

1 0

[galaxyproject/galaxy] 97ba92: external_runner: load json template first
by GitHub 11 Nov '18

11 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97ba92f3cffd0c17353595c61bd5d22c7a4e8c4e https://github.com/galaxyproject/galaxy/commit/97ba92f3cffd0c17353595c61bd5… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M scripts/drmaa_external_runner.py Log Message: ----------- external_runner: load json template first if the JSON is loaded first the cluster_files_directory does not need to be accessible by the real user (ie all users) Commit: be76d9f8017efa14f133ee8fb49c0f3b490bdd2a https://github.com/galaxyproject/galaxy/commit/be76d9f8017efa14f133ee8fb49c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-11 (Sun, 11 Nov 2018) Changed paths: M scripts/drmaa_external_runner.py Log Message: ----------- Merge pull request #6995 from bernt-matthias/topic/external-runner-json-load-order external_runner: load json template first Compare: https://github.com/galaxyproject/galaxy/compare/acfbca32dd7d...be76d9f8017e **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] 773a9b: Fix fastq set_metadata on python 3
by GitHub 10 Nov '18

10 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 773a9bef892ede8f464a14de5f89469045568ec3 https://github.com/galaxyproject/galaxy/commit/773a9bef892ede8f464a14de5f89… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-10 (Sat, 10 Nov 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Fix fastq set_metadata on python 3 Commit: acfbca32dd7dc381750f6a9362b48ddaa4abd5a5 https://github.com/galaxyproject/galaxy/commit/acfbca32dd7dc381750f6a9362b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-10 (Sat, 10 Nov 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #7001 from mvdbeek/fastq_fix Fix set_peek for fastg datatype Compare: https://github.com/galaxyproject/galaxy/compare/e98f63caf2d2...acfbca32dd7d **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] 199fe7: Allow saving workflows with input parameters
by GitHub 10 Nov '18

10 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 199fe7e0fccbeeb55501bad54f8ae4e44e7c100c https://github.com/galaxyproject/galaxy/commit/199fe7e0fccbeeb55501bad54f8a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Allow saving workflows with input parameters Commit: 638b1b7581d38b9044e17937f308c82fd36663ee https://github.com/galaxyproject/galaxy/commit/638b1b7581d38b9044e17937f308… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Allow inserting input parameter into workflow Commit: c09d1bc150775909f0e2a8f1c48ad0b2b70afea0 https://github.com/galaxyproject/galaxy/commit/c09d1bc150775909f0e2a8f1c48a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- WIP: add StepParameter inputs to workflow editor In the current state when a text, integer, float, boolean or boolean parameter is set as "Set at Runtime" a new connectable input appears for the tool node, to which a Parameter can be properly dragged and connected. This still needs a little more separation from data inputs/outputs, and the new connection isn't persisted in a meaningful way. Commit: 99c270fd77367a813af6202465d5453be78ac4eb https://github.com/galaxyproject/galaxy/commit/99c270fd77367a813af6202465d5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix rebuilding parameter node Commit: b0d64a8f09e6dc3d29c069edcb2abe77ee9c3662 https://github.com/galaxyproject/galaxy/commit/b0d64a8f09e6dc3d29c069edcb2a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix selecting the correct item from select list select lists don't take a `value` argument. Commit: c624cc4bce8b7b2bea9eaf61ecbf8bea485c4640 https://github.com/galaxyproject/galaxy/commit/c624cc4bce8b7b2bea9eaf61ecbf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix getting correct type Commit: 83a25c90e66b52890fcd8ad9288059d87b4f4932 https://github.com/galaxyproject/galaxy/commit/83a25c90e66b52890fcd8ad92880… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Fix restoring saved non-data connections in workflow editor Commit: 4e3004bb250f86b8c16a1c94c8599f497488e732 https://github.com/galaxyproject/galaxy/commit/4e3004bb250f86b8c16a1c94c859… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix node.addOuputParameter Commit: e135fac159e80549ce611a40f4c66598f51632d2 https://github.com/galaxyproject/galaxy/commit/e135fac159e80549ce611a40f4c6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Don't render data inputs on parameter_input node Commit: 0340dcb18a99d9d7984eb7566b3826290fe90025 https://github.com/galaxyproject/galaxy/commit/0340dcb18a99d9d7984eb7566b38… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- More defensive runtime check Commit: 5a5b4abb5bd4b1b142601a94b4498556c4f14946 https://github.com/galaxyproject/galaxy/commit/5a5b4abb5bd4b1b142601a94b449… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Allow loading in test-data workfows Commit: 4812586156b4cf01fe8ee1cb743306cc91ba2c84 https://github.com/galaxyproject/galaxy/commit/4812586156b4cf01fe8ee1cb7433… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js Log Message: ----------- Add label to input parameters without labels. Commit: dbe4033abe74035082b510c862c7729212367341 https://github.com/galaxyproject/galaxy/commit/dbe4033abe74035082b510c862c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-icons.js Log Message: ----------- Give parameter inputs a workflow icon. Commit: 00b8776db521cab884a107f8b66441690f644f88 https://github.com/galaxyproject/galaxy/commit/00b8776db521cab884a107f8b664… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Convert raw parameters from map into formal parameters when invoking wfs. Commit: d74b959419a667b2ff3192c9fde07a2cddc5e90d https://github.com/galaxyproject/galaxy/commit/d74b959419a667b2ff3192c9fde0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Revert non-data connection handling, send connections unfiltered to editor. Commit: 85d777dbe704ccdbf71898853e542c1c2df05303 https://github.com/galaxyproject/galaxy/commit/85d777dbe704ccdbf71898853e54… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py Log Message: ----------- Separate RuntimeValue into RuntimeValue and ConnectedValue. Use ConnectedValue values to determine what non-data parameters to display connections for. Commit: dd8d74f364770a1272555a3753f5d1e1288315e1 https://github.com/galaxyproject/galaxy/commit/dd8d74f364770a1272555a3753f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Unify data/non-data input/output handling for workflow editor. Don't treat data and non-data inputs/outputs different at the API boundary or at the workflow-manager.js level. Keep differences at the level of walking inputs/outputs in the workflow module on the backend and at the terminal definition (models and views) level on the frontend. Make the code and interfaces more consistent in my opinion and is more compatible with future directions I'd like to take things with mix-mode inputs/outputs for CWL. Commit: 5a99ebd5af9d68f028b86d295846a1c4cefccfb4 https://github.com/galaxyproject/galaxy/commit/5a99ebd5af9d68f028b86d295846… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Remove filtering of connections for workflow editor. Things not matching should be handled there. Commit: 29950be83f8240acba05685b4a057b38d803b445 https://github.com/galaxyproject/galaxy/commit/29950be83f8240acba05685b4a05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Workflow editor testing for step parameters/connections. - Fixes and refactoring for existing input tests (toward reuse). - Add simple test for non-data input. Commit: f12e548872b0087b4ba8b5828bc80b6aa10207e4 https://github.com/galaxyproject/galaxy/commit/f12e548872b0087b4ba8b5828bc8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/workflow/run.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_run.py Log Message: ----------- Step parameter workflow run test case and fix. Commit: e98f63caf2d2adfd7857ff9fcba6df0b5923b668 https://github.com/galaxyproject/galaxy/commit/e98f63caf2d2adfd7857ff9fcba6… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-10 (Sat, 10 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #6925 from jmchilton/workflow_step_parameters_3 Add workflow step parameters to workflow editor (try 3) Compare: https://github.com/galaxyproject/galaxy/compare/b57c25622b74...e98f63caf2d2 **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] 35bc1b: Typos in admin docs.
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 35bc1b387a3371e46b42c16c7b5664c33474d4fd https://github.com/galaxyproject/galaxy/commit/35bc1b387a3371e46b42c16c7b56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Typos in admin docs. Commit: e9ab7add6e8e3ab31cf858e344bd0c568fc5fd83 https://github.com/galaxyproject/galaxy/commit/e9ab7add6e8e3ab31cf858e344bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Another typo in admin/nginx Commit: b57c25622b74b51b70cfe71d477a86a1f85b05a9 https://github.com/galaxyproject/galaxy/commit/b57c25622b74b51b70cfe71d477a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/nginx.md Log Message: ----------- Merge pull request #6999 from dannon/typo_fix Fix several typos in admin docs. Compare: https://github.com/galaxyproject/galaxy/compare/cfacaae8b50c...b57c25622b74 **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] 215993: Merge remote-tracking branch 'galaxyproject/dev' i...
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 21599376501e7a740f8d2700b2463024f02ca58e https://github.com/galaxyproject/galaxy/commit/21599376501e7a740f8d2700b246… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M .ci/jenkins/selenium-py3/run_tests.sh M .gitignore M .travis.yml M Makefile M client/.babelrc R client/GruntFile.js M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md A client/galaxy/images/Armitagep_manhattan.png A client/galaxy/images/Armitagep_qqplot.png A client/galaxy/images/add_icon.png A client/galaxy/images/add_icon_dark.png A client/galaxy/images/aggregate_history1.png A client/galaxy/images/aggregate_history2.png A client/galaxy/images/bar_chart.png A client/galaxy/images/base_bg.png A client/galaxy/images/bed_warn.png A client/galaxy/images/button_bar_bg_light.png A client/galaxy/images/circle.py A client/galaxy/images/closebox.png A client/galaxy/images/dat_points_table_brows_1.png A client/galaxy/images/data_empty.png A client/galaxy/images/data_error.png A client/galaxy/images/data_ok.png A client/galaxy/images/data_queued.png A client/galaxy/images/data_running.gif A client/galaxy/images/ddarrowsplit.png A client/galaxy/images/delete.gif A client/galaxy/images/delete_tag_icon_gray.png A client/galaxy/images/delete_tag_icon_white.png A client/galaxy/images/documents-stack-faded.png A client/galaxy/images/documents-stack.png A client/galaxy/images/done_message_icon.png A client/galaxy/images/dropdownarrow.png A client/galaxy/images/error_bg.png A client/galaxy/images/error_icon.svg A 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test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py A test/unit/test_compression_util.py M test/unit/test_galaxy_mapping.py M test/unit/test_remote_shell.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_toolbox_filters.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_workflow_progress.py A tools/cloud/send.py A tools/cloud/send.xml M tools/data_source/upload.py M tools/data_source/upload.xml M tools/extract/extract_genomic_dna.py M tools/filters/convert_characters.py M tools/filters/grep.py M tools/filters/uniq.py M tools/stats/filtering.py M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into dev Commit: d5b46e99d234a615d06b1376bf57e1ada49154c9 https://github.com/galaxyproject/galaxy/commit/d5b46e99d234a615d06b1376bf57… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/sequence.fastg Log Message: ----------- datatype_fastg FASTG is a format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty. http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf This format can be an output for metagenomics applications metapades and megahit. It is a required input for Graph2Pro-var application that generates putative protein sequences for the variant assemblies described by the FASTG format file. Commit: a3badf62478f975bb0f9b1ca339d14f74116c4be https://github.com/galaxyproject/galaxy/commit/a3badf62478f975bb0f9b1ca339d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Update config/datatypes_conf.xml.sample Co-Authored-By: jj-umn <jj(a)umn.edu> Commit: 8dc824e4831aca566d65e3f488cd8f0e8224c014 https://github.com/galaxyproject/galaxy/commit/8dc824e4831aca566d65e3f488cd… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Update sequence.py Fix typo for properties. Commit: 4c71bb43a36ad173718c2f89b4fabaa632e11515 https://github.com/galaxyproject/galaxy/commit/4c71bb43a36ad173718c2f89b4fa… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Update sequence.py remove extraneous line that was pasted in. Commit: f21a3dd81572d341ae28e2bd62512fb849e6fecc https://github.com/galaxyproject/galaxy/commit/f21a3dd81572d341ae28e2bd6251… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-11-08 (Thu, 08 Nov 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Update sequence.py Line after header must not be empty or start with '>' Commit: e5c5cd284d6ed927667f330bfd579092f281e5d6 https://github.com/galaxyproject/galaxy/commit/e5c5cd284d6ed927667f330bfd57… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Update sequence.py Fix a couple of typos. Commit: cfacaae8b50c9650e4d365063a177fbda9c0895c https://github.com/galaxyproject/galaxy/commit/cfacaae8b50c9650e4d365063a17… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/sequence.fastg Log Message: ----------- Merge pull request #6987 from jj-umn/dev datatype_fastg Compare: https://github.com/galaxyproject/galaxy/compare/3ed0ce862bf9...cfacaae8b50c **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] 9f8c29: Use virtualenv when conda is on PATH
by GitHub 09 Nov '18

09 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f8c29520df53ca42e241d69718ddd2e1d37a987 https://github.com/galaxyproject/galaxy/commit/9f8c29520df53ca42e241d69718d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M scripts/common_startup.sh Log Message: ----------- Use virtualenv when conda is on PATH This uses our proper pinned requirements and is sginificantly easier to set up and maintain. Commit: 3ed0ce862bf9397aefa3b3d58552e2013fcd098c https://github.com/galaxyproject/galaxy/commit/3ed0ce862bf9397aefa3b3d58552… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M scripts/common_startup.sh Log Message: ----------- Merge pull request #6975 from mvdbeek/conda_run_sh Use virtualenv when conda is on PATH Compare: https://github.com/galaxyproject/galaxy/compare/5f2c785d66f7...3ed0ce862bf9 **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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