- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 603b23: Force standard HTTPTransport for sentry -- this pl...
by GitHub 13 Jul '18

13 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 603b2365b6a261e5603c618c637cf8458e667007 https://github.com/galaxyproject/galaxy/commit/603b2365b6a261e5603c618c637c… Author: Dannon Baker <dannon.baker(a)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: f94a073e86be608916ec7ae79285da06ee82483b https://github.com/galaxyproject/galaxy/commit/f94a073e86be608916ec7ae79285… Author: guerler <aysam.guerler(a)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: 3fe88a9bfe1b010ca30ffac32e5c4e200398c48e https://github.com/galaxyproject/galaxy/commit/3fe88a9bfe1b010ca30ffac32e5c… Author: Nicola Soranzo <nicola.soranzo(a)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/bc95f2563601635cfa1daa686b3d… Author: Devon Ryan <dpryan79(a)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/23666c94a22b816bc5238e4a22c7… Author: John Chilton <jmchilton(a)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/93fc3a63507d6cd7c85a99ad62e7… Author: John Chilton <jmchilton(a)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/20565a2b8517fbc4c54524fa0ae1… Author: John Chilton <jmchilton(a)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: dfc996c8d6b8e166ae17fe8502f9e4f9252b6106 https://github.com/galaxyproject/galaxy/commit/dfc996c8d6b8e166ae17fe8502f9… Author: Nicola Soranzo <nicola.soranzo(a)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: 2abb01b6cbb11f28a7f6a838c97b8540b62e45fb https://github.com/galaxyproject/galaxy/commit/2abb01b6cbb11f28a7f6a838c97b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/web/base/controller.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/fa43f2c2b2e7...2abb01b6cbb1 **NOTE:** This service 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] bc95f2: Fix the --log-file option in the job handlers
by GitHub 13 Jul '18

13 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: bc95f2563601635cfa1daa686b3d5c4e3ebb51ea https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… Author: Devon Ryan <dpryan79(a)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/23666c94a22b816bc5238e4a22c7… Author: John Chilton <jmchilton(a)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: dfc996c8d6b8e166ae17fe8502f9e4f9252b6106 https://github.com/galaxyproject/galaxy/commit/dfc996c8d6b8e166ae17fe8502f9… Author: Nicola Soranzo <nicola.soranzo(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/20565a2b8517...dfc996c8d6b8 **NOTE:** This service 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] 29de69: Add period to the list of allowed characters in us...
by GitHub 12 Jul '18

12 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 29de694b1f272e58cf84c8998c6e6181e25b9fd2 https://github.com/galaxyproject/galaxy/commit/29de694b1f272e58cf84c8998c6e… Author: Oleksandr Moskalenko <om(a)rc.ufl.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Add period to the list of allowed characters in user names Commit: fa43f2c2b2e7f047b2d8a27b9bca313f67637c75 https://github.com/galaxyproject/galaxy/commit/fa43f2c2b2e7f047b2d8a27b9bca… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #6365 from moskalenko/dev Add period to the list of allowed characters in user names Compare: https://github.com/galaxyproject/galaxy/compare/30feac0c4ca4...fa43f2c2b2e7 **NOTE:** This service 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] 4da672: Added fix to ensure that original ftp files that h...
by GitHub 12 Jul '18

12 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4da67218c166374016c239397db2c10f3a388e66 https://github.com/galaxyproject/galaxy/commit/4da67218c166374016c239397db2… Author: takadonet <philipmabon(a)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: 30feac0c4ca4488caa4d7d00beee698a6e465cdf https://github.com/galaxyproject/galaxy/commit/30feac0c4ca4488caa4d7d00beee… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #6494 from phac-nml/fix_ftp_upload_purge Fix ftp_upload_purge in galaxy.yml Compare: https://github.com/galaxyproject/galaxy/compare/2cccf7c23fc5...30feac0c4ca4 **NOTE:** This service 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] b06932: Allow : in tag values for PJA setting.
by GitHub 12 Jul '18

12 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b0693203a1ed4d755f6fac261dd98bdddb6da6b2 https://github.com/galaxyproject/galaxy/commit/b0693203a1ed4d755f6fac261dd9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Allow : in tag values for PJA setting. Based on #5457, certain paths to creating tag values with : must already work - just not when parsing from a raw string I guess. Commit: b45ce119401b6ef36a19c1bd21c84856ebc074e2 https://github.com/galaxyproject/galaxy/commit/b45ce119401b6ef36a19c1bd21c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Centralize logic for determining which tags get auto-propagated. Commit: 0280713c43442a412cf6294b57caf1c12160322f https://github.com/galaxyproject/galaxy/commit/0280713c43442a412cf6294b57ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Auto-propagate group tags - the way name tags are propagated. Commit: 2cccf7c23fc57e4e633af2b1703d7d4a034f5850 https://github.com/galaxyproject/galaxy/commit/2cccf7c23fc57e4e633af2b1703d… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6491 from jmchilton/auto_group_tags Implement ``group:`` tags (toward multi-factor analysis with group tagging) Compare: https://github.com/galaxyproject/galaxy/compare/0674af824d2c...2cccf7c23fc5 **NOTE:** This service 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] d91ad7: small improvement to the too xsd docs
by GitHub 12 Jul '18

12 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d91ad7d6275cf004b670a11a23a6258e51500c89 https://github.com/galaxyproject/galaxy/commit/d91ad7d6275cf004b670a11a23a6… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- small improvement to the too xsd docs Commit: cabd6a11bed38eaa69175a8505c4f6071478bd5f https://github.com/galaxyproject/galaxy/commit/cabd6a11bed38eaa69175a8505c4… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- added <output> to snippet Commit: 5bac0eff82d5fa4931834082baeb220c701fd5b5 https://github.com/galaxyproject/galaxy/commit/5bac0eff82d5fa4931834082baeb… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Update galaxy.xsd Commit: 0674af824d2ccfa8cdc924b6387e0112912bbb47 https://github.com/galaxyproject/galaxy/commit/0674af824d2ccfa8cdc924b6387e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6490 from bernt-matthias/topic/xsd-doc-discover-improvement small improvement to the too xsd docs regarding discovered_datasets Compare: https://github.com/galaxyproject/galaxy/compare/6fc937a3d8b4...0674af824d2c **NOTE:** This service 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] ac87a1: Install migmap version 1.0.2 for the pRESTO suite
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ac87a19c3df23214462dfa85338a6b691a8e2dba https://github.com/galaxyproject/usegalaxy-playbook/commit/ac87a19c3df23214… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Install migmap version 1.0.2 for the pRESTO suite **NOTE:** This service 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] 8ad57f: Fix for rendering multiple dependent dynamic selec...
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8ad57fa1f18453c1cd94249b881b93a557639dfd https://github.com/galaxyproject/galaxy/commit/8ad57fa1f18453c1cd94249b881b… Author: greg <ghv2(a)psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix for rendering multiple dependent dynamic select lists where choosing an option in the first refreshes the options in the second Commit: 6fc937a3d8b46f3620b73f3e057d9b6ba5422540 https://github.com/galaxyproject/galaxy/commit/6fc937a3d8b46f3620b73f3e057d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6374 from gregvonkuster/multi_dynamic_select Fix for rendering multiple dependent dynamic select lists Compare: https://github.com/galaxyproject/galaxy/compare/f33770096c03...6fc937a3d8b4 **NOTE:** This service 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] 603b23: Force standard HTTPTransport for sentry -- this pl...
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 603b2365b6a261e5603c618c637cf8458e667007 https://github.com/galaxyproject/galaxy/commit/603b2365b6a261e5603c618c637c… Author: Dannon Baker <dannon.baker(a)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: 20565a2b8517fbc4c54524fa0ae127c2f6aaefb0 https://github.com/galaxyproject/galaxy/commit/20565a2b8517fbc4c54524fa0ae1… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/93fc3a63507d...20565a2b8517 **NOTE:** This service 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] f94a07: Make sure that the workflow step has a proper stat...
by GitHub 11 Jul '18

11 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f94a073e86be608916ec7ae79285da06ee82483b https://github.com/galaxyproject/galaxy/commit/f94a073e86be608916ec7ae79285… Author: guerler <aysam.guerler(a)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: 93fc3a63507d6cd7c85a99ad62e71b14d4d6265e https://github.com/galaxyproject/galaxy/commit/93fc3a63507d6cd7c85a99ad62e7… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/3fe88a9bfe1b...93fc3a63507d **NOTE:** This service 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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