Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a6eb37b47261f6f3f77573ac9610a8a5ddc4e0d https://github.com/galaxyproject/galaxy/commit/4a6eb37b47261f6f3f77573ac9610... Author: E Rasche hxr@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/abfb69252a733d967dddcf7f3b6ea... Author: E Rasche hxr@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/75b923b677825a78076f453311358... Author: E Rasche hxr@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/d23bb5689ed97c9e8c3c0bb12c192... Author: E Rasche hxr@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/fc4bcc0a7e9fc7b01c4a4a0691180... Author: Nate Coraor nate@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/6872325d80c26ca352ee3d68b4727... Author: E Rasche hxr@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/ea22750604bb2b14a437eddc6ab34... Author: Ann Loraine aloraine@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/ffe7981cc2f902fafa1dc3c8d3203... Author: Helena Rasche hxr@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/fbbbb472977094fb89be1cbde818c... Author: Helena Rasche hxr@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/8992620ee19e4b6dbd58dfa411eec... Author: Helena Rasche hxr@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/92e4ef8d93375c5283d92bab05873... Author: Helena Rasche hxr@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/da1a6085ac10681a2f983245c52f9... Author: Helena Rasche hxr@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/b4bd972b71ca5a535f07942c1e16a... Author: Helena Rasche hxr@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/82e5d7d50c00ee13640c24e832d3a... Author: Helena Rasche hxr@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/3cfe8040b6f239a53bf1e048104c7... Author: Helena Rasche hxr@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/590fb5c48bf340837eb5e70fb3f60... Author: Helena Rasche hxr@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/5d048486ac56e500abad5c46032dc... Author: Helena Rasche hxr@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/80e0ffccb24be54edbfef9e6b2c2d... Author: Martin Cech marten@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/7681a4d33e035e9cc8b918211e296... Author: Martin Cech marten@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/2a8a793013c0ec46024c64d633491... Author: Helena Rasche hxr@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/3d39e0fad0418edecf0169beff778... Author: Helena Rasche hxr@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/ee985e6bbcfe8c3cf3e2fdcdfb825... Author: Helena Rasche hxr@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/01248c24118e293921ab92550cec3... Author: Helena Rasche hxr@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/6cc20f263491fb570bdbcc29911d2... Author: Helena Rasche hxr@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/a8e75e0f602283e8fc506f3321830... Author: Helena Rasche hxr@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/15ceedfbc059494da18e077336f02... Author: Helena Rasche hxr@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/157cc410e2b0a2a8ab1476d4ba4b3... Author: Helena Rasche hxr@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/3dbbc56e9689deabd62d71a3db926... Author: Helena Rasche hxr@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/c122b3f57306399b2f9d993d61e22... Author: Helena Rasche hxr@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/ff007c4b72c504999fde2cf09f891... Author: Helena Rasche hxr@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/2005c102e629d5dd5082c26facd22... Author: Helena Rasche hxr@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/2f351bf3a77e842b5790e5993e456... Author: Helena Rasche hxr@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/41e6910df2b101551b4fc8ebc55ed... Author: Helena Rasche hxr@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/b381adb5fe6d76950ebc56c063564... Author: Helena Rasche hxr@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/effd5f92f245f13faa53ceeb41734... Author: Nicola Soranzo nicola.soranzo@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/85e5d7fcd3261d3283ff3fa78d0c2... Author: Nicola Soranzo nicola.soranzo@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/efb0f02d345cb9a5d415fa4dd9ac1... Author: Nicola Soranzo nicola.soranzo@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/1dc47498463f886bdf23fe4cf3db7... Author: Martin Cech marten@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/cba219cc02ce54c0cac77d915a144... Author: Martin Cech marten@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/b4de30b5fc6056bd8c9dfb7898332... Author: John Chilton jmchilton@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/a310b0a121e19c126b2c5bdaa093b... Author: Dannon Baker dannon.baker@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/48de2ecf21d5b68596e308b2a3769... Author: Dannon Baker dannon.baker@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/cdbae706e603f57af4a795907ef2c... Author: John Chilton jmchilton@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/242d5459e13c502527971dc2b21ed... Author: John Chilton jmchilton@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/4531d80dbcaf5671fdcb56627f3cc... Author: Nicola Soranzo nicola.soranzo@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/bf51c8352648b4a56a4a162deee4c... Author: John Chilton jmchilton@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/5903edd4dab84e076da2a4f01129c... Author: Dannon dannon.baker@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/7532de99c9c64fa92667f80f64198... Author: Dannon dannon.baker@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/8f5fc79db6561a15e2eba5ead5471... Author: Dannon dannon.baker@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/ec83035c2a4c7037afd56c615a3f5... Author: Martin Cech marten@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/f8bfb821692e2bd88bd6dea705206... Author: Martin Cech marten@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/3a9a46f772ba9c7d2ed96af3096e3... Author: Martin Cech marten@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/b114b1d6bafc334dc63b08d6654b2... Author: Nicola Soranzo nicola.soranzo@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/c3f9e0c2a7bb5273228d790b62eaf... Author: Nicola Soranzo nicola.soranzo@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.