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

[galaxyproject/galaxy] 4a6eb3: Add config option
by GitHub 16 May '18

16 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a6eb37b47261f6f3f77573ac9610a8a5ddc4e0d https://github.com/galaxyproject/galaxy/commit/4a6eb37b47261f6f3f77573ac961… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Add config option Commit: abfb69252a733d967dddcf7f3b6ea69f61645ff8 https://github.com/galaxyproject/galaxy/commit/abfb69252a733d967dddcf7f3b6e… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Some progress on this Commit: 75b923b677825a78076f4533113580ad3386b357 https://github.com/galaxyproject/galaxy/commit/75b923b677825a78076f45331135… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- do not log usernames Commit: d23bb5689ed97c9e8c3c0bb12c1926594bf7ad3c https://github.com/galaxyproject/galaxy/commit/d23bb5689ed97c9e8c3c0bb12c19… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Redact docker logs Commit: fc4bcc0a7e9fc7b01c4a4a069118077d01c236c5 https://github.com/galaxyproject/galaxy/commit/fc4bcc0a7e9fc7b01c4a4a069118… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Handle Slurm 17.11's OUT_OF_MEMORY job state. Commit: 6872325d80c26ca352ee3d68b4727cf59299d239 https://github.com/galaxyproject/galaxy/commit/6872325d80c26ca352ee3d68b472… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Remove user IDs from job names Commit: ea22750604bb2b14a437eddc6ab34dd9d4d9fba7 https://github.com/galaxyproject/galaxy/commit/ea22750604bb2b14a437eddc6ab3… Author: Ann Loraine <aloraine(a)uncc.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml Log Message: ----------- Change BioViz URL to http://bioviz.org/galaxy.html from http://bioviz.org/igb/galaxy.html Commit: ffe7981cc2f902fafa1dc3c8d3203ec3a2f8b4df https://github.com/galaxyproject/galaxy/commit/ffe7981cc2f902fafa1dc3c8d320… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- broken access Commit: fbbbb472977094fb89be1cbde818cdee0e5961a9 https://github.com/galaxyproject/galaxy/commit/fbbbb472977094fb89be1cbde818… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- override expose_user_{name,email} Commit: 8992620ee19e4b6dbd58dfa411eecfba306613bf https://github.com/galaxyproject/galaxy/commit/8992620ee19e4b6dbd58dfa411ee… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- hash email/username Commit: 92e4ef8d93375c5283d92bab0587339237be2436 https://github.com/galaxyproject/galaxy/commit/92e4ef8d93375c5283d92bab0587… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix job running Commit: da1a6085ac10681a2f983245c52f96563a742efc https://github.com/galaxyproject/galaxy/commit/da1a6085ac10681a2f983245c52f… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Also wipe out roles Commit: b4bd972b71ca5a535f07942c1e16ac96962a3298 https://github.com/galaxyproject/galaxy/commit/b4bd972b71ca5a535f07942c1e16… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- update documentation Commit: 82e5d7d50c00ee13640c24e832d3a733a463abff https://github.com/galaxyproject/galaxy/commit/82e5d7d50c00ee13640c24e832d3… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- add custom logger Commit: 3cfe8040b6f239a53bf1e048104c7d9af7958149 https://github.com/galaxyproject/galaxy/commit/3cfe8040b6f239a53bf1e048104c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- allow tests to pass Commit: 590fb5c48bf340837eb5e70fb3f608382f9f8ebf https://github.com/galaxyproject/galaxy/commit/590fb5c48bf340837eb5e70fb3f6… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/auth/providers/localdb.py Log Message: ----------- remove print Commit: 5d048486ac56e500abad5c46032dc962097bd9d5 https://github.com/galaxyproject/galaxy/commit/5d048486ac56e500abad5c46032d… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Rework into separate permissions per @jmchilton suggestion Commit: 80e0ffccb24be54edbfef9e6b2c2d00ae24f6141 https://github.com/galaxyproject/galaxy/commit/80e0ffccb24be54edbfef9e6b2c2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- add mock config to fix unittests; fix lint Commit: 7681a4d33e035e9cc8b918211e2961b42c621cf1 https://github.com/galaxyproject/galaxy/commit/7681a4d33e035e9cc8b918211e29… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- replace forgotten older config option Commit: 2a8a793013c0ec46024c64d63349172e04ee059f https://github.com/galaxyproject/galaxy/commit/2a8a793013c0ec46024c64d63349… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Mirror option across all schemas Commit: 3d39e0fad0418edecf0169beff778236bf7e4a84 https://github.com/galaxyproject/galaxy/commit/3d39e0fad0418edecf0169beff77… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- read policy options Commit: ee985e6bbcfe8c3cf3e2fdcdfb8257c999612a86 https://github.com/galaxyproject/galaxy/commit/ee985e6bbcfe8c3cf3e2fdcdfb82… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst Log Message: ----------- Update documentation Commit: 01248c24118e293921ab92550cec32007e19ab2f https://github.com/galaxyproject/galaxy/commit/01248c24118e293921ab92550cec… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- document a bunch of undocumented options Commit: 6cc20f263491fb570bdbcc29911d278b4e48d2a1 https://github.com/galaxyproject/galaxy/commit/6cc20f263491fb570bdbcc29911d… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst Log Message: ----------- start writing compliance documentation Commit: a8e75e0f602283e8fc506f332183011758b8de74 https://github.com/galaxyproject/galaxy/commit/a8e75e0f602283e8fc506f332183… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Need to fail safely unfortunately if we cannot access app Commit: 15ceedfbc059494da18e077336f0264e65e5a7cb https://github.com/galaxyproject/galaxy/commit/15ceedfbc059494da18e077336f0… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Unbreak toolshed user deletion Commit: 157cc410e2b0a2a8ab1476d4ba4b3210afd2e535 https://github.com/galaxyproject/galaxy/commit/157cc410e2b0a2a8ab1476d4ba4b… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/util/admin_util.py Log Message: ----------- duplicate deletion/redaction logic Commit: 3dbbc56e9689deabd62d71a3db926d697d681891 https://github.com/galaxyproject/galaxy/commit/3dbbc56e9689deabd62d71a3db92… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Redact addresses as well Commit: c122b3f57306399b2f9d993d61e22054ee0586a9 https://github.com/galaxyproject/galaxy/commit/c122b3f57306399b2f9d993d61e2… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- better docs Commit: ff007c4b72c504999fde2cf09f891cb2fdc543d3 https://github.com/galaxyproject/galaxy/commit/ff007c4b72c504999fde2cf09f89… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- rename main variable Commit: 2005c102e629d5dd5082c26facd2282fbfb1015b https://github.com/galaxyproject/galaxy/commit/2005c102e629d5dd5082c26facd2… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- force user_deletion on for GDPR users Commit: 2f351bf3a77e842b5790e5993e4565be998ca3ff https://github.com/galaxyproject/galaxy/commit/2f351bf3a77e842b5790e5993e45… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst Log Message: ----------- rebuild configuratoin Commit: 41e6910df2b101551b4fc8ebc55ed3f1ff0b39b6 https://github.com/galaxyproject/galaxy/commit/41e6910df2b101551b4fc8ebc55e… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- document more gdpr stuff :( Commit: b381adb5fe6d76950ebc56c0635649a33cfdc819 https://github.com/galaxyproject/galaxy/commit/b381adb5fe6d76950ebc56c06356… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- automatically add to logging config block Commit: effd5f92f245f13faa53ceeb41734124d14a0eb8 https://github.com/galaxyproject/galaxy/commit/effd5f92f245f13faa53ceeb4173… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M test/functional/tools/job_properties.xml Log Message: ----------- Lint job_properties test tool Commit: 85e5d7fcd3261d3283ff3fa78d0c2b78fe429f4b https://github.com/galaxyproject/galaxy/commit/85e5d7fcd3261d3283ff3fa78d0c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix required tools to run workflow API tests Commit: efb0f02d345cb9a5d415fa4dd9ac1bf8ca507f5d https://github.com/galaxyproject/galaxy/commit/efb0f02d345cb9a5d415fa4dd9ac… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Hide replacement datasets when rerunning a failed dataset in a mapped-over collection Commit: 1dc47498463f886bdf23fe4cf3db75a69018a480 https://github.com/galaxyproject/galaxy/commit/1dc47498463f886bdf23fe4cf3db… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- iteration of gdpr compliance docs Commit: cba219cc02ce54c0cac77d915a144f91e9b6377f https://github.com/galaxyproject/galaxy/commit/cba219cc02ce54c0cac77d915a14… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- fix import order Commit: b4de30b5fc6056bd8c9dfb7898332b1264c159e6 https://github.com/galaxyproject/galaxy/commit/b4de30b5fc6056bd8c9dfb789833… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- Small fixes for upload flags (auto_decompress, check_content, space_to_tab). Commit: a310b0a121e19c126b2c5bdaa093b2f2bb056c5a https://github.com/galaxyproject/galaxy/commit/a310b0a121e19c126b2c5bdaa093… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix minor typo in rule builder. Commit: 48de2ecf21d5b68596e308b2a37696eff54e37d0 https://github.com/galaxyproject/galaxy/commit/48de2ecf21d5b68596e308b2a376… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- client-format Commit: cdbae706e603f57af4a795907ef2cdfc0b058482 https://github.com/galaxyproject/galaxy/commit/cdbae706e603f57af4a795907ef2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/datatypes/upload_util.py M lib/galaxy/tools/data_fetch.py M test/api/test_tools_upload.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Respect auto_decompress in fetch API, synchronize upload APIs. Commit: 242d5459e13c502527971dc2b21ed1ac4ab119cd https://github.com/galaxyproject/galaxy/commit/242d5459e13c502527971dc2b21e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- "Fix" RuleBuilder to auto decompress compressed files. Work arounds just aren't there yet. Commit: 4531d80dbcaf5671fdcb56627f3cc948cd710c4e https://github.com/galaxyproject/galaxy/commit/4531d80dbcaf5671fdcb56627f3c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- When re-running a failed dataset collection element, update JobToOutputDatasetCollectionAssociation to the new job Otherwise, if re-running fails once, then re-running it again successfully will let the other workflow jobs resume, but the collection element is not replaced and the collection remains red. Commit: bf51c8352648b4a56a4a162deee4c37ee8e551db https://github.com/galaxyproject/galaxy/commit/bf51c8352648b4a56a4a162deee4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6140 from dannon/minor_typo [18.05] Minor typo in rule builder Commit: 5903edd4dab84e076da2a4f01129ca2c231646f5 https://github.com/galaxyproject/galaxy/commit/5903edd4dab84e076da2a4f01129… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml Log Message: ----------- Merge pull request #6109 from aloraine/update_bioviz_link Update BioViz URL Commit: 7532de99c9c64fa92667f80f641984005fd85f01 https://github.com/galaxyproject/galaxy/commit/7532de99c9c64fa92667f80f6419… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py M test/functional/tools/job_properties.xml Log Message: ----------- Merge pull request #6137 from nsoranzo/release_18.01_fix_workflow_resume_with_mapped_over_input [18.01] Fixes for workflow resume with mapped over inputs Commit: 8f5fc79db6561a15e2eba5ead5471fcd61defb81 https://github.com/galaxyproject/galaxy/commit/8f5fc79db6561a15e2eba5ead547… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/tools/data_fetch.py M test/api/test_tools_upload.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6141 from jmchilton/rules_fix_10 [18.05] "Fix" rule builder to auto decompress uploaded files. Commit: ec83035c2a4c7037afd56c615a3f5351d1e7e539 https://github.com/galaxyproject/galaxy/commit/ec83035c2a4c7037afd56c615a3f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6007 from natefoo/slurm-oom [18.01] Handle Slurm 17.11's OUT_OF_MEMORY job state Commit: f8bfb821692e2bd88bd6dea7052062b6c0422fe3 https://github.com/galaxyproject/galaxy/commit/f8bfb821692e2bd88bd6dea70520… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- fix what :eagle: :eyes: spotted Commit: 3a9a46f772ba9c7d2ed96af3096e3f8a55fe3b01 https://github.com/galaxyproject/galaxy/commit/3a9a46f772ba9c7d2ed96af3096e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/tool_shed/util/admin_util.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #6069 from erasche/gdpr [18.05] GDPR Compliance Mode Commit: b114b1d6bafc334dc63b08d6654b24bec7ab87d5 https://github.com/galaxyproject/galaxy/commit/b114b1d6bafc334dc63b08d6654b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py M test/functional/tools/job_properties.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: c3f9e0c2a7bb5273228d790b62eaf8626687f420 https://github.com/galaxyproject/galaxy/commit/c3f9e0c2a7bb5273228d790b62ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/tool_shed/util/admin_util.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/functional/tools/job_properties.xml M test/integration/test_upload_configuration_options.py M test/unit/unittest_utils/galaxy_mock.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/867cdd144448...c3f9e0c2a7bb **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] fc4bcc: Handle Slurm 17.11's OUT_OF_MEMORY job state.
by GitHub 16 May '18

16 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: fc4bcc0a7e9fc7b01c4a4a069118077d01c236c5 https://github.com/galaxyproject/galaxy/commit/fc4bcc0a7e9fc7b01c4a4a069118… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Handle Slurm 17.11's OUT_OF_MEMORY job state. Commit: effd5f92f245f13faa53ceeb41734124d14a0eb8 https://github.com/galaxyproject/galaxy/commit/effd5f92f245f13faa53ceeb4173… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M test/functional/tools/job_properties.xml Log Message: ----------- Lint job_properties test tool Commit: 85e5d7fcd3261d3283ff3fa78d0c2b78fe429f4b https://github.com/galaxyproject/galaxy/commit/85e5d7fcd3261d3283ff3fa78d0c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix required tools to run workflow API tests Commit: efb0f02d345cb9a5d415fa4dd9ac1bf8ca507f5d https://github.com/galaxyproject/galaxy/commit/efb0f02d345cb9a5d415fa4dd9ac… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Hide replacement datasets when rerunning a failed dataset in a mapped-over collection Commit: 4531d80dbcaf5671fdcb56627f3cc948cd710c4e https://github.com/galaxyproject/galaxy/commit/4531d80dbcaf5671fdcb56627f3c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- When re-running a failed dataset collection element, update JobToOutputDatasetCollectionAssociation to the new job Otherwise, if re-running fails once, then re-running it again successfully will let the other workflow jobs resume, but the collection element is not replaced and the collection remains red. Commit: 7532de99c9c64fa92667f80f641984005fd85f01 https://github.com/galaxyproject/galaxy/commit/7532de99c9c64fa92667f80f6419… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py M test/functional/tools/job_properties.xml Log Message: ----------- Merge pull request #6137 from nsoranzo/release_18.01_fix_workflow_resume_with_mapped_over_input [18.01] Fixes for workflow resume with mapped over inputs Commit: ec83035c2a4c7037afd56c615a3f5351d1e7e539 https://github.com/galaxyproject/galaxy/commit/ec83035c2a4c7037afd56c615a3f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6007 from natefoo/slurm-oom [18.01] Handle Slurm 17.11's OUT_OF_MEMORY job state Commit: b114b1d6bafc334dc63b08d6654b24bec7ab87d5 https://github.com/galaxyproject/galaxy/commit/b114b1d6bafc334dc63b08d6654b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py M test/functional/tools/job_properties.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/3a9a46f772ba...b114b1d6bafc **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] 02ffbd: Make cache_directory configurable in mulled singlu...
by GitHub 16 May '18

16 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 02ffbdd7b1c65c30c00ea86e499ad1b36759a555 https://github.com/galaxyproject/galaxy/commit/02ffbdd7b1c65c30c00ea86e499a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Make cache_directory configurable in mulled singluarity resolvers. Commit: 867cdd144448810571bcf23888027800a292c344 https://github.com/galaxyproject/galaxy/commit/867cdd144448810571bcf2388802… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Merge pull request #6122 from jmchilton/singularity_mulled_container_cache Make cache_directory configurable in mulled Singluarity resolvers. Compare: https://github.com/galaxyproject/galaxy/compare/ab05ac94755d...867cdd144448 **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] 4a6eb3: Add config option
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 4a6eb37b47261f6f3f77573ac9610a8a5ddc4e0d https://github.com/galaxyproject/galaxy/commit/4a6eb37b47261f6f3f77573ac961… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Add config option Commit: abfb69252a733d967dddcf7f3b6ea69f61645ff8 https://github.com/galaxyproject/galaxy/commit/abfb69252a733d967dddcf7f3b6e… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Some progress on this Commit: 75b923b677825a78076f4533113580ad3386b357 https://github.com/galaxyproject/galaxy/commit/75b923b677825a78076f45331135… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- do not log usernames Commit: d23bb5689ed97c9e8c3c0bb12c1926594bf7ad3c https://github.com/galaxyproject/galaxy/commit/d23bb5689ed97c9e8c3c0bb12c19… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Redact docker logs Commit: 6872325d80c26ca352ee3d68b4727cf59299d239 https://github.com/galaxyproject/galaxy/commit/6872325d80c26ca352ee3d68b472… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Remove user IDs from job names Commit: ffe7981cc2f902fafa1dc3c8d3203ec3a2f8b4df https://github.com/galaxyproject/galaxy/commit/ffe7981cc2f902fafa1dc3c8d320… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py Log Message: ----------- broken access Commit: fbbbb472977094fb89be1cbde818cdee0e5961a9 https://github.com/galaxyproject/galaxy/commit/fbbbb472977094fb89be1cbde818… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- override expose_user_{name,email} Commit: 8992620ee19e4b6dbd58dfa411eecfba306613bf https://github.com/galaxyproject/galaxy/commit/8992620ee19e4b6dbd58dfa411ee… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- hash email/username Commit: 92e4ef8d93375c5283d92bab0587339237be2436 https://github.com/galaxyproject/galaxy/commit/92e4ef8d93375c5283d92bab0587… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix job running Commit: da1a6085ac10681a2f983245c52f96563a742efc https://github.com/galaxyproject/galaxy/commit/da1a6085ac10681a2f983245c52f… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Also wipe out roles Commit: b4bd972b71ca5a535f07942c1e16ac96962a3298 https://github.com/galaxyproject/galaxy/commit/b4bd972b71ca5a535f07942c1e16… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- update documentation Commit: 82e5d7d50c00ee13640c24e832d3a733a463abff https://github.com/galaxyproject/galaxy/commit/82e5d7d50c00ee13640c24e832d3… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- add custom logger Commit: 3cfe8040b6f239a53bf1e048104c7d9af7958149 https://github.com/galaxyproject/galaxy/commit/3cfe8040b6f239a53bf1e048104c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- allow tests to pass Commit: 590fb5c48bf340837eb5e70fb3f608382f9f8ebf https://github.com/galaxyproject/galaxy/commit/590fb5c48bf340837eb5e70fb3f6… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/auth/providers/localdb.py Log Message: ----------- remove print Commit: 5d048486ac56e500abad5c46032dc962097bd9d5 https://github.com/galaxyproject/galaxy/commit/5d048486ac56e500abad5c46032d… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Rework into separate permissions per @jmchilton suggestion Commit: 80e0ffccb24be54edbfef9e6b2c2d00ae24f6141 https://github.com/galaxyproject/galaxy/commit/80e0ffccb24be54edbfef9e6b2c2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- add mock config to fix unittests; fix lint Commit: 7681a4d33e035e9cc8b918211e2961b42c621cf1 https://github.com/galaxyproject/galaxy/commit/7681a4d33e035e9cc8b918211e29… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- replace forgotten older config option Commit: 2a8a793013c0ec46024c64d63349172e04ee059f https://github.com/galaxyproject/galaxy/commit/2a8a793013c0ec46024c64d63349… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- Mirror option across all schemas Commit: 3d39e0fad0418edecf0169beff778236bf7e4a84 https://github.com/galaxyproject/galaxy/commit/3d39e0fad0418edecf0169beff77… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- read policy options Commit: ee985e6bbcfe8c3cf3e2fdcdfb8257c999612a86 https://github.com/galaxyproject/galaxy/commit/ee985e6bbcfe8c3cf3e2fdcdfb82… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst Log Message: ----------- Update documentation Commit: 01248c24118e293921ab92550cec32007e19ab2f https://github.com/galaxyproject/galaxy/commit/01248c24118e293921ab92550cec… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/config_schema.yml Log Message: ----------- document a bunch of undocumented options Commit: 6cc20f263491fb570bdbcc29911d278b4e48d2a1 https://github.com/galaxyproject/galaxy/commit/6cc20f263491fb570bdbcc29911d… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst Log Message: ----------- start writing compliance documentation Commit: a8e75e0f602283e8fc506f332183011758b8de74 https://github.com/galaxyproject/galaxy/commit/a8e75e0f602283e8fc506f332183… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Need to fail safely unfortunately if we cannot access app Commit: 15ceedfbc059494da18e077336f0264e65e5a7cb https://github.com/galaxyproject/galaxy/commit/15ceedfbc059494da18e077336f0… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Unbreak toolshed user deletion Commit: 157cc410e2b0a2a8ab1476d4ba4b3210afd2e535 https://github.com/galaxyproject/galaxy/commit/157cc410e2b0a2a8ab1476d4ba4b… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/util/admin_util.py Log Message: ----------- duplicate deletion/redaction logic Commit: 3dbbc56e9689deabd62d71a3db926d697d681891 https://github.com/galaxyproject/galaxy/commit/3dbbc56e9689deabd62d71a3db92… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Redact addresses as well Commit: c122b3f57306399b2f9d993d61e22054ee0586a9 https://github.com/galaxyproject/galaxy/commit/c122b3f57306399b2f9d993d61e2… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- better docs Commit: ff007c4b72c504999fde2cf09f891cb2fdc543d3 https://github.com/galaxyproject/galaxy/commit/ff007c4b72c504999fde2cf09f89… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- rename main variable Commit: 2005c102e629d5dd5082c26facd2282fbfb1015b https://github.com/galaxyproject/galaxy/commit/2005c102e629d5dd5082c26facd2… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- force user_deletion on for GDPR users Commit: 2f351bf3a77e842b5790e5993e4565be998ca3ff https://github.com/galaxyproject/galaxy/commit/2f351bf3a77e842b5790e5993e45… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst Log Message: ----------- rebuild configuratoin Commit: 41e6910df2b101551b4fc8ebc55ed3f1ff0b39b6 https://github.com/galaxyproject/galaxy/commit/41e6910df2b101551b4fc8ebc55e… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- document more gdpr stuff :( Commit: b381adb5fe6d76950ebc56c0635649a33cfdc819 https://github.com/galaxyproject/galaxy/commit/b381adb5fe6d76950ebc56c06356… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- automatically add to logging config block Commit: 1dc47498463f886bdf23fe4cf3db75a69018a480 https://github.com/galaxyproject/galaxy/commit/1dc47498463f886bdf23fe4cf3db… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- iteration of gdpr compliance docs Commit: cba219cc02ce54c0cac77d915a144f91e9b6377f https://github.com/galaxyproject/galaxy/commit/cba219cc02ce54c0cac77d915a14… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- fix import order Commit: f8bfb821692e2bd88bd6dea7052062b6c0422fe3 https://github.com/galaxyproject/galaxy/commit/f8bfb821692e2bd88bd6dea70520… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/admin/special_topics/gdpr_compliance.rst Log Message: ----------- fix what :eagle: :eyes: spotted Commit: 3a9a46f772ba9c7d2ed96af3096e3f8a55fe3b01 https://github.com/galaxyproject/galaxy/commit/3a9a46f772ba9c7d2ed96af3096e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/tool_shed/util/admin_util.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #6069 from erasche/gdpr [18.05] GDPR Compliance Mode Compare: https://github.com/galaxyproject/galaxy/compare/8f5fc79db656...3a9a46f772ba **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] fc4bcc: Handle Slurm 17.11's OUT_OF_MEMORY job state.
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: fc4bcc0a7e9fc7b01c4a4a069118077d01c236c5 https://github.com/galaxyproject/galaxy/commit/fc4bcc0a7e9fc7b01c4a4a069118… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Handle Slurm 17.11's OUT_OF_MEMORY job state. Commit: ec83035c2a4c7037afd56c615a3f5351d1e7e539 https://github.com/galaxyproject/galaxy/commit/ec83035c2a4c7037afd56c615a3f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6007 from natefoo/slurm-oom [18.01] Handle Slurm 17.11's OUT_OF_MEMORY job state Compare: https://github.com/galaxyproject/galaxy/compare/7532de99c9c6...ec83035c2a4c **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] b4de30: Small fixes for upload flags (auto_decompress, che...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: b4de30b5fc6056bd8c9dfb7898332b1264c159e6 https://github.com/galaxyproject/galaxy/commit/b4de30b5fc6056bd8c9dfb789833… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- Small fixes for upload flags (auto_decompress, check_content, space_to_tab). Commit: cdbae706e603f57af4a795907ef2cdfc0b058482 https://github.com/galaxyproject/galaxy/commit/cdbae706e603f57af4a795907ef2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/datatypes/upload_util.py M lib/galaxy/tools/data_fetch.py M test/api/test_tools_upload.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Respect auto_decompress in fetch API, synchronize upload APIs. Commit: 242d5459e13c502527971dc2b21ed1ac4ab119cd https://github.com/galaxyproject/galaxy/commit/242d5459e13c502527971dc2b21e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- "Fix" RuleBuilder to auto decompress compressed files. Work arounds just aren't there yet. Commit: 8f5fc79db6561a15e2eba5ead5471fcd61defb81 https://github.com/galaxyproject/galaxy/commit/8f5fc79db6561a15e2eba5ead547… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/tools/data_fetch.py M test/api/test_tools_upload.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6141 from jmchilton/rules_fix_10 [18.05] "Fix" rule builder to auto decompress uploaded files. Compare: https://github.com/galaxyproject/galaxy/compare/5903edd4dab8...8f5fc79db656 **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] effd5f: Lint job_properties test tool
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: effd5f92f245f13faa53ceeb41734124d14a0eb8 https://github.com/galaxyproject/galaxy/commit/effd5f92f245f13faa53ceeb4173… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M test/functional/tools/job_properties.xml Log Message: ----------- Lint job_properties test tool Commit: 85e5d7fcd3261d3283ff3fa78d0c2b78fe429f4b https://github.com/galaxyproject/galaxy/commit/85e5d7fcd3261d3283ff3fa78d0c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix required tools to run workflow API tests Commit: efb0f02d345cb9a5d415fa4dd9ac1bf8ca507f5d https://github.com/galaxyproject/galaxy/commit/efb0f02d345cb9a5d415fa4dd9ac… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Hide replacement datasets when rerunning a failed dataset in a mapped-over collection Commit: 4531d80dbcaf5671fdcb56627f3cc948cd710c4e https://github.com/galaxyproject/galaxy/commit/4531d80dbcaf5671fdcb56627f3c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- When re-running a failed dataset collection element, update JobToOutputDatasetCollectionAssociation to the new job Otherwise, if re-running fails once, then re-running it again successfully will let the other workflow jobs resume, but the collection element is not replaced and the collection remains red. Commit: 7532de99c9c64fa92667f80f641984005fd85f01 https://github.com/galaxyproject/galaxy/commit/7532de99c9c64fa92667f80f6419… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py M test/functional/tools/job_properties.xml Log Message: ----------- Merge pull request #6137 from nsoranzo/release_18.01_fix_workflow_resume_with_mapped_over_input [18.01] Fixes for workflow resume with mapped over inputs Compare: https://github.com/galaxyproject/galaxy/compare/3137d84ad7d7...7532de99c9c6 **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] 6919da: Merge remote-tracking branch 'galaxyproject/dev' i...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6919da46d876768902b51639b1784c2df797f543 https://github.com/galaxyproject/galaxy/commit/6919da46d876768902b51639b178… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/api/run_tests.sh M .ci/jenkins/selenium-compose/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/galaxy.js A client/galaxy/scripts/layout/communication-server-view.js R client/galaxy/scripts/layout/generic-nav-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/scratchbook.js M client/galaxy/scripts/legacy/grid/grid-view.js R client/galaxy/scripts/libs/bootstrap-tour.js R client/galaxy/scripts/libs/bootstrap.js A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A 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M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-item-li.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/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/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M 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config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_destinations.yml.sample M config/tool_shed.yml.sample M config/user_preferences_extra_conf.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M create_db.sh M doc/Makefile M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/nginx.md M doc/source/admin/reports_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/conf.py A doc/source/conf.versioning.py M doc/source/lib/galaxy.web.framework.middleware.rst A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A 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test/functional/twilltestcase.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_data_manager_table_reload.py A test/integration/test_scripts.py A test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.py M test/manual/launch_and_run.sh R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/jobs/test_mapper.py M test/unit/managers/test_HistoryManager.py A test/unit/test_rule_utils.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into dev Commit: c3982fdf4ca9cf12595e02be4f08a074ec52f60c https://github.com/galaxyproject/galaxy/commit/c3982fdf4ca9cf12595e02be4f08… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py Log Message: ----------- Add blib MS spectral library datatype blib is a SQlite schema for MassSpec spectral library Commit: c5828aa67c02689060cbb500fb32bf0ca0585f8f https://github.com/galaxyproject/galaxy/commit/c5828aa67c02689060cbb500fb32… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.blib Log Message: ----------- blib datatype add test file: test.blib include blib version in metadata Commit: 3b027af3df512194929fa6a979b111fccd5b9f6d https://github.com/galaxyproject/galaxy/commit/3b027af3df512194929fa6a979b1… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix flake8 errors Commit: a4ab17cb0db618b8182a0c48726b1fcce8d17bfe https://github.com/galaxyproject/galaxy/commit/a4ab17cb0db618b8182a0c48726b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Add blib test case for supplied test data, fix RetentionTimes not always available. Commit: 3ec6753f0db67de8fefc162ece7502fe47286d35 https://github.com/galaxyproject/galaxy/commit/3ec6753f0db67de8fefc162ece75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- No need to specify these default entries I don't think. Most new datatypes don't get added here, I'm not really sure what purpose these serve. Commit: ab05ac94755da11a400c2efd12b95b84ec1ecf15 https://github.com/galaxyproject/galaxy/commit/ab05ac94755da11a400c2efd12b9… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.blib Log Message: ----------- Merge pull request #6092 from jj-umn/dev Add blib datatype for Mass Spectrometry spectral library Compare: https://github.com/galaxyproject/galaxy/compare/e52802f8fd0e...ab05ac94755d **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/infrastructure-playbook] ba14fe: Disable UnkillableStepTimeout as cgroups failing t...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ba14fe325c5b844b035d2eb33aa6cc5ca1b7182e https://github.com/galaxyproject/infrastructure-playbook/commit/ba14fe325c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Disable UnkillableStepTimeout as cgroups failing to delete seem to have all occurred after it. **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] ea2275: Change BioViz URL to http://bioviz.org/galaxy.html...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: ea22750604bb2b14a437eddc6ab34dd9d4d9fba7 https://github.com/galaxyproject/galaxy/commit/ea22750604bb2b14a437eddc6ab3… Author: Ann Loraine <aloraine(a)uncc.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml Log Message: ----------- Change BioViz URL to http://bioviz.org/galaxy.html from http://bioviz.org/igb/galaxy.html Commit: 5903edd4dab84e076da2a4f01129ca2c231646f5 https://github.com/galaxyproject/galaxy/commit/5903edd4dab84e076da2a4f01129… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml Log Message: ----------- Merge pull request #6109 from aloraine/update_bioviz_link Update BioViz URL Compare: https://github.com/galaxyproject/galaxy/compare/bf51c8352648...5903edd4dab8 **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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