Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 676886195d1fbe17cdff16af8acad6f5c2115ee1 https://github.com/galaxyproject/galaxy/commit/676886195d1fbe17cdff16af8acad... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-05-28 (Mon, 28 May 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix non-strict tabular relabel operation Commit: 3b3deb314f4a78684bea9707d2f0d856e306f006 https://github.com/galaxyproject/galaxy/commit/3b3deb314f4a78684bea9707d2f0d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Use strict mode when testing strict mode ... Commit: 4661b6e8831c2cae86b7d9725431e71bacd22168 https://github.com/galaxyproject/galaxy/commit/4661b6e8831c2cae86b7d9725431e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Allow invalid optional param values for old tools For tools with profile < 18.09 we return None for provided, but illegal default values. This can happen when referencing columns of an optional dataset for instance, as experienced in https://github.com/galaxyproject/tools-iuc/pull/1842. This used to pass prior to 18.05 because we would always return the value if there were no legal values. This was changed in https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302fd... where we would only allow this in workflow building mode. Commit: 470299a2ce6ef1e5d894a0247bd43f24fd463d41 https://github.com/galaxyproject/galaxy/commit/470299a2ce6ef1e5d894a0247bd43... Author: John Chilton <jmchilton@gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Merge pull request #6234 from mvdbeek/fix_relabel_non_strict [18.01] Fix non-strict tabular relabel operation Commit: eed703eef8b3884f70019070210633f0e033b39b https://github.com/galaxyproject/galaxy/commit/eed703eef8b3884f7001907021063... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Fix share with another user in 18.05 Commit: 48fafa8096fd179e9c74c56bac7be9b042cbade8 https://github.com/galaxyproject/galaxy/commit/48fafa8096fd179e9c74c56bac7be... Author: John Chilton <jmchilton@gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Merge pull request #6358 from dannon/1805sharingfix [18.01] Fix 'share with another user' Commit: c6403acd0f18196c0453a90fe89ccf861d7a28d6 https://github.com/galaxyproject/galaxy/commit/c6403acd0f18196c0453a90fe89cc... Author: John Chilton <jmchilton@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix logging bug. Commit: d0a0fa8319e5b32e222e261b1b9f0242e210d1c7 https://github.com/galaxyproject/galaxy/commit/d0a0fa8319e5b32e222e261b1b9f0... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml M templates/sharing_base.mako Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 6d5be41b320510d6e2d163399a3a6e30d6f9bda0 https://github.com/galaxyproject/galaxy/commit/6d5be41b320510d6e2d163399a3a6... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #6366 from jmchilton/job_log_bug [18.05] Fix small bug in logging output name in job finish. Commit: 603b2365b6a261e5603c618c637cf8458e667007 https://github.com/galaxyproject/galaxy/commit/603b2365b6a261e5603c618c637cf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Force standard HTTPTransport for sentry -- this plays nicer with a wider array of uwsgi configurations Commit: 572f38d1fb47e914ad10766007c855786e1643a2 https://github.com/galaxyproject/galaxy/commit/572f38d1fb47e914ad10766007c85... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- move the sanitization to the try/except block as it may fail (and it did, on Main) Commit: f94a073e86be608916ec7ae79285da06ee82483b https://github.com/galaxyproject/galaxy/commit/f94a073e86be608916ec7ae79285d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Make sure that the workflow step has a proper state available Commit: d28ab2a4f31b363c236a02a535cc43ab049190ca https://github.com/galaxyproject/galaxy/commit/d28ab2a4f31b363c236a02a535cc4... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6377 from martenson/catch-sanitization-faults [18.05] Catch sanitization faults Commit: 9967639bac92eb3f7103794663f41b88f11baa9c https://github.com/galaxyproject/galaxy/commit/9967639bac92eb3f7103794663f41... Author: guerler <aysam.guerler@gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Comma-separate tool names in missing tools error message Commit: 22d383c39842e0a0198cf2d37ad3832ea1838769 https://github.com/galaxyproject/galaxy/commit/22d383c39842e0a0198cf2d37ad38... Author: Dannon <dannon.baker@gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #6378 from guerler/commaseperror [18.05] Comma-separate tool names in missing tools error message Commit: fa2b6baef71984c0559c53ff5750d1fe9b77163e https://github.com/galaxyproject/galaxy/commit/fa2b6baef71984c0559c53ff5750d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Revert "Remove bam to bai converter" This reverts commit 7e2727bc0a74868198e7e457f99df3d1e39f1ddb. Commit: 5f24794efdad757b77c75c3aa111da7a11c5bb47 https://github.com/galaxyproject/galaxy/commit/5f24794efdad757b77c75c3aa111d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add basic .bai datatype Commit: 36706e9eb38728c91c1da2a4cf66ff49f3f44d72 https://github.com/galaxyproject/galaxy/commit/36706e9eb38728c91c1da2a4cf66f... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge pull request #6385 from dannon/revert-baiconverter-removal [18.01] Revert "Remove bam to bai converter" Commit: e0c269291a20ae3a01a24bae930012baba3bb10c https://github.com/galaxyproject/galaxy/commit/e0c269291a20ae3a01a24bae93001... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-06-23 (Sat, 23 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 6654a837527797971b28fd2cbb092d7081c918b9 https://github.com/galaxyproject/galaxy/commit/6654a837527797971b28fd2cbb092... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Hack around #6299. Commit: 39d7cf2eb73177532237ad38a8a75095d1be4428 https://github.com/galaxyproject/galaxy/commit/39d7cf2eb73177532237ad38a8a75... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6433 from jmchilton/hack_6299 [18.05] decode potential encoded id Commit: 0c97d4ff5c83318551319524582619656ae848b8 https://github.com/galaxyproject/galaxy/commit/0c97d4ff5c8331855131952458261... Author: thobalose <lose.thoba@gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 Commit: 3fe88a9bfe1b010ca30ffac32e5c4e200398c48e https://github.com/galaxyproject/galaxy/commit/3fe88a9bfe1b010ca30ffac32e5c4... Author: Nicola Soranzo <nicola.soranzo@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6465 from dannon/backport-gie-static-again [18.05] Backport of IE static url fix (to actual 18.05) Commit: bc95f2563601635cfa1daa686b3d5c4e3ebb51ea https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d5... Author: Devon Ryan <dpryan79@gmail.com> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix the --log-file option in the job handlers (cherry picked from commit 97c344a17a0188a687629103feefcdf03af8e768) Commit: 23666c94a22b816bc5238e4a22c759a11265f7aa https://github.com/galaxyproject/galaxy/commit/23666c94a22b816bc5238e4a22c75... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6477 from natefoo/backport-pr-6351 [18.01] Fix the --log-file option in the job handlers Commit: 93fc3a63507d6cd7c85a99ad62e71b14d4d6265e https://github.com/galaxyproject/galaxy/commit/93fc3a63507d6cd7c85a99ad62e71... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6369 from guerler/pages [18.05] Make sure that the workflow step has a proper state available Commit: 20565a2b8517fbc4c54524fa0ae127c2f6aaefb0 https://github.com/galaxyproject/galaxy/commit/20565a2b8517fbc4c54524fa0ae12... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #6375 from dannon/sentry_transport_fix [18.05] Specify standard HTTPTransport for Sentry Commit: 4b0ae30a83aeb86a821ec15cfa87e6af7e160a03 https://github.com/galaxyproject/galaxy/commit/4b0ae30a83aeb86a821ec15cfa87e... Author: takadonet <philipmabon@gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Added fix to ensure that original ftp files that have been uploaded are purged if set in galaxy.yml with flag ftp_upload_purge. Address issue #6492 Commit: dfc996c8d6b8e166ae17fe8502f9e4f9252b6106 https://github.com/galaxyproject/galaxy/commit/dfc996c8d6b8e166ae17fe8502f9e... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: fd33c5c6d6aa2478654da74c7e80efdcf31e09a7 https://github.com/galaxyproject/galaxy/commit/fd33c5c6d6aa2478654da74c7e80e... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #6497 from martenson/backport-takadonet [18.05] backport ftp purge fix Commit: 7b8e4f9e740725861951535d59e50243e4a0b2e0 https://github.com/galaxyproject/galaxy/commit/7b8e4f9e740725861951535d59e50... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt Log Message: ----------- Fix empty datatypes. Commit: ef702e1458f746299710e9ce5afb7b350b61f91c https://github.com/galaxyproject/galaxy/commit/ef702e1458f746299710e9ce5afb7... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt Log Message: ----------- Merge pull request #6510 from nsoranzo/release_18.05_backport_29f8e29b0bf5d50c0b735aa707d2a61623cc805b [18.05] Fix infinite loop in uploads Commit: a8b9899681939286a03badd85c9c71f972958a18 https://github.com/galaxyproject/galaxy/commit/a8b9899681939286a03badd85c9c7... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml Log Message: ----------- Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0 Since v2.27.0 (see https://github.com/arq5x/bedtools2/commit/4d188435777cfbd6ada7394ee78fde37f0... ), `bedtools genomecov` emits this warning: ``` ***** *****WARNING: Genome (-g) files are ignored when BAM input is provided. ***** ``` if both `-ibam` and `-g` option are specified, which causes the converters to always fail. Also: - Add `detect_errors="aggressive"` to `<command/>` to prevent future warnings from creating other issues. - Fix input format in `CONVERTER_sam_to_bigwig_0`. Commit: 50b34185394cc38159c33ca98b74e1418a7b1e55 https://github.com/galaxyproject/galaxy/commit/50b34185394cc38159c33ca98b74e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml Log Message: ----------- Merge pull request #6528 from nsoranzo/release_18.05_fix_CONVERTER_bam_to_bigwig_0 [18.05] Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0 Commit: 9794d835e507c31d82aa82c79e86998154419980 https://github.com/galaxyproject/galaxy/commit/9794d835e507c31d82aa82c79e869... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Fix to_dict with io_details=True for tools with collection outputs. Fixes #6537 and includes a test case. Commit: 5f19b8752dfd940efd156de1a0c1a4e6e914800b https://github.com/galaxyproject/galaxy/commit/5f19b8752dfd940efd156de1a0c1a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Fix empty handling rule. Commit: a88bf0a2bee152c859f229c2a017b8a03d96b8d8 https://github.com/galaxyproject/galaxy/commit/a88bf0a2bee152c859f229c2a017b... Author: Dannon <dannon.baker@gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6264 from mvdbeek/allow_optional_and_invalid_parameter_values [18.05] Allow invalid optional param values for tools profile versions < 18.09 Commit: 0a9010156e30a20d730324807c3e238510f44b77 https://github.com/galaxyproject/galaxy/commit/0a9010156e30a20d730324807c3e2... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6538 from jmchilton/tool_output_io [18.01] Fix to_dict with io_details=True for tools with collection outputs. Commit: 66e74d0e475ef6fd6f6de125b41f9990e274fbfb https://github.com/galaxyproject/galaxy/commit/66e74d0e475ef6fd6f6de125b41f9... Author: Dannon <dannon.baker@gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Merge pull request #6542 from jmchilton/1805_fix_empty_handling_rule_on_backend [18.05] Fix "filter empty" rule in Python rule handling framework. Commit: 9630699c21875199fec75bc3f607d5b81a224348 https://github.com/galaxyproject/galaxy/commit/9630699c21875199fec75bc3f607d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Simpler, more targeted fix for copy datasets dialog tag copies (will refactor in dev) Commit: ba47188f5e896d9f2bd6718796093f05e1c7aa9b https://github.com/galaxyproject/galaxy/commit/ba47188f5e896d9f2bd6718796093... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Introduce test for auto-labelling subworkflow workflow outputs Commit: 21fd74e640c2ba872d98259ea213e20e99c6ba75 https://github.com/galaxyproject/galaxy/commit/21fd74e640c2ba872d98259ea213e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use subworkflow index when setting auto-label Previously this would reference the parent workflow index, while the get_data module would use the subworkflow index. This means defining workflows worked fine, but executing would fail when trying to find the output to replace. Using the subworkflow index here seems like the correct thing to do. Fixes https://github.com/galaxyproject/galaxy/issues/6560 Commit: ffdf674c75d49235edee80090fe4235ac9b0d86e https://github.com/galaxyproject/galaxy/commit/ffdf674c75d49235edee80090fe42... Author: guerler <aysam.guerler@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix worklfow run link for extracted workflows Commit: 6c7b9a3c7d4459b171fa806f2912d49e44ccd5bd https://github.com/galaxyproject/galaxy/commit/6c7b9a3c7d4459b171fa806f2912d... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #6532 from dannon/fix-dataset-copy-tags [18.05] Fix dataset copy tags Commit: 6d9df51f36e293bd1ce20d3bf9e21a5646ff5b94 https://github.com/galaxyproject/galaxy/commit/6d9df51f36e293bd1ce20d3bf9e21... Author: Dannon <dannon.baker@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery [18.01] Use subworkflow index when setting auto-label Commit: d7959568f85b45f378f6972d971075f7169cffc4 https://github.com/galaxyproject/galaxy/commit/d7959568f85b45f378f6972d97107... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: ea085b07a0efdd5322aab3bb613fc363b71967b5 https://github.com/galaxyproject/galaxy/commit/ea085b07a0efdd5322aab3bb613fc... Author: Dannon <dannon.baker@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6571 from guerler/fix_link [18.05] Fix workflow run link for extracted workflows Compare: https://github.com/galaxyproject/galaxy/compare/bcf105cbb37a...ea085b07a0ef **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.