- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 6b6815: Updated lastz to version 1.3.1
by GitHub 17 May '18

17 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6b6815bf44cf65183a4f1847c6fe90aaf92ff60e https://github.com/galaxyproject/usegalaxy-playbook/commit/6b6815bf44cf6518… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-05-17 (Thu, 17 May 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated lastz to version 1.3.1 **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] d2dc22: Use RetryActionExecutor when executing commands vi...
by GitHub 16 May '18

16 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: d2dc22d97f35ff1c4cc780ce03c3a6e41ded86cb https://github.com/galaxyproject/galaxy/commit/d2dc22d97f35ff1c4cc780ce03c3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Use RetryActionExecutor when executing commands via paramiko This should work around issues like ``` galaxy.jobs.runners ERROR 2018-05-16 10:15:55,522 [p:13768,w:0,m:1] [ShellRunner.work_thread-3] (34130) Unhandled exception calling queue_job Traceback (most recent call last): File "lib/galaxy/jobs/runners/__init__.py", line 112, in run_next method(arg) File "lib/galaxy/jobs/runners/cli.py", line 94, in queue_job chmod_out = shell.execute("chmod +x %s" % tool_script) File "lib/galaxy/jobs/runners/util/cli/shell/rsh.py", line 77, in execute self.connect() File "lib/galaxy/jobs/runners/util/cli/shell/rsh.py", line 69, in connect timeout=self.timeout) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paramiko/client.py", line 424, in connect passphrase, File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paramiko/client.py", line 714, in _auth raise saved_exception SSHException: not a valid OPENSSH private key file ``` that can intermittently occur with rapid submission of many small jobs. Commit: 7029cb936a9f016a7f714dcbdc88709231ee8d5a https://github.com/galaxyproject/galaxy/commit/7029cb936a9f016a7f714dcbdc88… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Merge pull request #6149 from mvdbeek/fix_stuck_jobs_when_paramiko_fails [18.05] Use RetryActionExecutor when executing commands via paramiko Compare: https://github.com/galaxyproject/galaxy/compare/5c455c4472f8...7029cb936a9f **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] 11a31a: Update tool build API for implicit collection conv...
by GitHub 16 May '18

16 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 11a31a1ae70be3ae41fb04b38852cab87ded1bd9 https://github.com/galaxyproject/galaxy/commit/11a31a1ae70be3ae41fb04b38852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Update tool build API for implicit collection conversion. Commit: 5c455c4472f88cae48beab85864f970c49ea2544 https://github.com/galaxyproject/galaxy/commit/5c455c4472f88cae48beab85864f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #6144 from jmchilton/allow_implicit_conversion [18.05] Fix tool build API for implicit collection conversion. Compare: https://github.com/galaxyproject/galaxy/compare/206daec262d9...5c455c4472f8 **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]
by GitHub 16 May '18

16 May '18

Branch: refs/heads/master-toolshed Home: https://github.com/galaxyproject/galaxy **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]
by GitHub 16 May '18

16 May '18

Branch: refs/heads/toolshed_repo_updates Home: https://github.com/galaxyproject/galaxy **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]
by GitHub 16 May '18

16 May '18

Branch: refs/heads/bowtie2_link Home: https://github.com/galaxyproject/galaxy **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] 0c9fd0: Release notes for 18.05.
by GitHub 16 May '18

16 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 0c9fd0e6de6d884dc5324288d74bdf049bc57e3d https://github.com/galaxyproject/galaxy/commit/0c9fd0e6de6d884dc5324288d74b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: A doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst A doc/source/releases/18.05_new_viz.png A doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- Release notes for 18.05. Commit: 276858e38e8126332c0952b581c09a2034b6a8d8 https://github.com/galaxyproject/galaxy/commit/276858e38e8126332c0952b581c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst Log Message: ----------- Fixes to the 18.05 release thanks to @nsoranzo's review. Commit: f3e49fb1e16ea063bd64de9f59914bf1ba2ada5c https://github.com/galaxyproject/galaxy/commit/f3e49fb1e16ea063bd64de9f5991… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- One more typo Commit: 63d4ea900b0fe8f1c3e653ebff33d7d9c3c25d05 https://github.com/galaxyproject/galaxy/commit/63d4ea900b0fe8f1c3e653ebff33… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst R doc/source/releases/18.05_new_viz.png Log Message: ----------- add most important PRs added Commit: 5d6249ec6fb45db681ad727c63612d20cb40a013 https://github.com/galaxyproject/galaxy/commit/5d6249ec6fb45db681ad727c6361… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- add security and breaking changes to release notes Commit: 77e187ddd1d6571de72f4a67a4fc7eeb148ae14c https://github.com/galaxyproject/galaxy/commit/77e187ddd1d6571de72f4a67a4fc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- match styling with older RN Commit: d70aadd6d10337e0cc43df325f52a8ce2ec31376 https://github.com/galaxyproject/galaxy/commit/d70aadd6d10337e0cc43df325f52… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- add minor tinies Commit: c4f74c19f3d5b3f550fe384a94bd524d1e93acfc https://github.com/galaxyproject/galaxy/commit/c4f74c19f3d5b3f550fe384a94bd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- add more breaking changes Commit: 04d1536edff9d9d467a8158ca536fdffecf097bb https://github.com/galaxyproject/galaxy/commit/04d1536edff9d9d467a8158ca536… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M doc/source/releases/18.05.rst Log Message: ----------- Fix typos Commit: 82dce758f1ad7b6d9d517531eea5497e9ac5ed3f https://github.com/galaxyproject/galaxy/commit/82dce758f1ad7b6d9d517531eea5… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: M doc/source/releases/18.05_announce.rst Log Message: ----------- Small fixes Commit: 206daec262d974bb8e50a091da91a102cb35c022 https://github.com/galaxyproject/galaxy/commit/206daec262d974bb8e50a091da91… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: A doc/source/releases/18.05.rst M doc/source/releases/18.05_announce.rst A doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #6006 from jmchilton/release_18.05_release_notes [18.05] Release notes for 18.05. Compare: https://github.com/galaxyproject/galaxy/compare/b114b1d6bafc...206daec262d9 **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] 3c965f: Remove unused retry.py, functionality provided in ...
by GitHub 16 May '18

16 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c965f526b6c2fd32453aef0c61e67def03891fd https://github.com/galaxyproject/galaxy/commit/3c965f526b6c2fd32453aef0c61e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: R lib/galaxy/jobs/runners/util/retry.py Log Message: ----------- Remove unused retry.py, functionality provided in pulsar Commit: b920875ff8b65bb9b5e4e13ac94e282cb09864fc https://github.com/galaxyproject/galaxy/commit/b920875ff8b65bb9b5e4e13ac94e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: R lib/galaxy/jobs/runners/util/drmaa/__init__.py Log Message: ----------- Drop DrmaaSessionFactory, unused and provided by pulsar Commit: 93d83c759d1ade726c407fa4e500455a838f6a47 https://github.com/galaxyproject/galaxy/commit/93d83c759d1ade726c407fa4e500… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-16 (Wed, 16 May 2018) Changed paths: R lib/galaxy/jobs/runners/util/drmaa/__init__.py R lib/galaxy/jobs/runners/util/retry.py Log Message: ----------- Merge pull request #6150 from mvdbeek/drop_unused_files Drop unused files Compare: https://github.com/galaxyproject/galaxy/compare/c3f9e0c2a7bb...93d83c759d1a **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 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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