- 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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[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.

1 0

[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.

1 0

[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.

1 0

[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 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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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lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_len.py R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py R 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lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py A lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/test.phylip M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R 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lib/galaxy/tools/repositories.py M lib/galaxy/tools/special_tools.py A lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py A lib/galaxy/util/create_history_template.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/logging/__init__.py M lib/galaxy/util/monitors.py M lib/galaxy/util/none_like.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/permutations.py A lib/galaxy/util/rules_dsl.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/script.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py A lib/galaxy/web/framework/helpers/tags.py R lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/message.py M lib/galaxy/webapps/config_manage.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py A 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lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/util/xml_util.py M 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templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako A test-data/1.csv A test-data/example-bag.zip A test-data/filter1_in6.bed A test-data/filter1_test6.bed A test-data/new_tags_1.txt A test-data/qname_sorted.bam A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv 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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[galaxyproject/galaxy] a310b0: Fix minor typo in rule builder.
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/3d6443b58bfa...bf51c8352648 **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] 69dce8: Use bootstrap-vue for Sharing.mako; convert alert,...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69dce8d38a5d151a4239d577def65eb88cc46f0f https://github.com/galaxyproject/galaxy/commit/69dce8d38a5d151a4239d577def6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Use bootstrap-vue for Sharing.mako; convert alert, drop unnecessary component style Commit: 824b5721b051cc490180d9204fbb61ef7a94ab48 https://github.com/galaxyproject/galaxy/commit/824b5721b051cc490180d9204fbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/managers/sharable.py Log Message: ----------- Fix bug where if username was null (which is allowed), the sharable manager blew up. Commit: 351709a6ba8cf07ac66e3ea7357f32c6d4c8c996 https://github.com/galaxyproject/galaxy/commit/351709a6ba8cf07ac66e3ea7357f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Swap to bsvue-buttons and table. If we really want this a table, we should restyle it. I think we can probably just kill the table, now that I've converted it. Commit: e52802f8fd0e349b8f222cbf56fd1d9ca4f63491 https://github.com/galaxyproject/galaxy/commit/e52802f8fd0e349b8f222cbf56fd… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/managers/sharable.py Log Message: ----------- Merge pull request #6132 from dannon/bsvue-sharing Sharing.vue bootstrapping and a bugfix Compare: https://github.com/galaxyproject/galaxy/compare/6a1057e95f5e...e52802f8fd0e **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] 616c1b: Add a text label length limit for select2's used i...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 616c1b971a01d7a7cf2967e1fea225c4466d13eb https://github.com/galaxyproject/galaxy/commit/616c1b971a01d7a7cf2967e1fea2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-12 (Sat, 12 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Add a text label length limit for select2's used in the upload dialog Reduce limit to a 100 characters Match encapsulated values in title string Commit: 8be2da03b52e819d5e4e4ac76dea983f4f0c2448 https://github.com/galaxyproject/galaxy/commit/8be2da03b52e819d5e4e4ac76dea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Improve dialog message while waiting for rule builder job. Commit: 788ed8aa43296537c6439d0fea7a5446ffe15da0 https://github.com/galaxyproject/galaxy/commit/788ed8aa43296537c6439d0fea7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Improve data initialization of rule builder for long term support. A mistake was made in the rush to rule-builder-all-the-stuffs - libraries, hdas, and FTP all initialized a different set of columns from the data (which is probably fine) but with no indication this was happening in the underlying rules (which is definitely not fine). To understand why this was a mistake and see why in the long term this hurts reproducibility, take loading rules for HDAs from the history panel as an example. In the initial implementation it would pre-initialize two columns - one for "hid" and one for "name" - any rules that were generated from there would start with an implicit assumption of two columns. This is a problem because if someone saves some rules and we (Galaxy developers) decide later on that name tag should be in the initial list but HID doesn't make sense and make that change - we basically are breaking all existing rules to support a very logical change in behavior. Likewise, Galaxy produces a hash with last modified date and size for each FTP entry - this is data we have and could stick in the rule builder by default - but if we change that over time existing FTP rules will break. It would be much more sustainable to instead include the initial column generation information in the initial rules generated - so that each of these modalities start in reality with an empty table and the initial set of rules describe what metadata to pull initial columns from. This way if you save a set of rules it will include the initial column choices, and if they are pasted in at some later point where columns are picked differently - the rules will still work because you are replacing the initial column definitions. The initial rules implementation didn't have this concept of loading columns from metadata - but this was added to support loading existing identifiers as part of the "Apply Rules to Existing Collection" tool. This commit extends that idea to do the same thing (but with different columns) when loading data from HDAs, FTP, and data libraries. Commit: c5ab87ee5909e0871fb62fcb2e82cdaecf5f8166 https://github.com/galaxyproject/galaxy/commit/c5ab87ee5909e0871fb62fcb2e82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Fix repeated additions of the separator, define vars. Commit: 9789aa7d637f8e0a1de558f01ef90a136f7e79a3 https://github.com/galaxyproject/galaxy/commit/9789aa7d637f8e0a1de558f01ef9… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Merge pull request #26 from dannon/max_select2_length Fix a minor bug, a little bit of cleanup. Commit: b0d730fa76cf8392a19cea5fe08a72aab2fccc2a https://github.com/galaxyproject/galaxy/commit/b0d730fa76cf8392a19cea5fe08a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select.js Log Message: ----------- Merge pull request #6130 from guerler/max_select2_length [18.05] Limit select2 text label length to 100 characters Commit: e5ea32465a64fed1acfa63b7385272a6f9ccee15 https://github.com/galaxyproject/galaxy/commit/e5ea32465a64fed1acfa63b73852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- More validation for rule builder. - Require a URL or FTP column for raw pasted data. - Require list identifiers if creating collections. - Require name in more scenerios that require a name. Commit: 5c036bc2647799c70b11b2a4e4ce0fae8d103cdc https://github.com/galaxyproject/galaxy/commit/5c036bc2647799c70b11b2a4e4ce… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6133 from jmchilton/rule_fixes_7 [18.05] Improve dialog message while waiting for rule builder job. Commit: 076e1ddaecd4f2744346c503b0108d8189f35bd1 https://github.com/galaxyproject/galaxy/commit/076e1ddaecd4f2744346c503b010… Author: Dannon <dannon.baker(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 #6136 from jmchilton/rule_fixes_9 [18.05] More validation for rule builder. Commit: 3d6443b58bfa0200cf775b569c542be326476493 https://github.com/galaxyproject/galaxy/commit/3d6443b58bfa0200cf775b569c54… 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 client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Merge pull request #6134 from jmchilton/rule_fixes_8 Improve data initialization of rule builder for long term support. Commit: 6a1057e95f5e46cbd676aaf6dbfe3a4df706d9c3 https://github.com/galaxyproject/galaxy/commit/6a1057e95f5e46cbd676aaf6dbfe… 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 M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7077851e9813...6a1057e95f5e **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.

1 0

[galaxyproject/galaxy] 788ed8: Improve data initialization of rule builder for lo...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 788ed8aa43296537c6439d0fea7a5446ffe15da0 https://github.com/galaxyproject/galaxy/commit/788ed8aa43296537c6439d0fea7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Improve data initialization of rule builder for long term support. A mistake was made in the rush to rule-builder-all-the-stuffs - libraries, hdas, and FTP all initialized a different set of columns from the data (which is probably fine) but with no indication this was happening in the underlying rules (which is definitely not fine). To understand why this was a mistake and see why in the long term this hurts reproducibility, take loading rules for HDAs from the history panel as an example. In the initial implementation it would pre-initialize two columns - one for "hid" and one for "name" - any rules that were generated from there would start with an implicit assumption of two columns. This is a problem because if someone saves some rules and we (Galaxy developers) decide later on that name tag should be in the initial list but HID doesn't make sense and make that change - we basically are breaking all existing rules to support a very logical change in behavior. Likewise, Galaxy produces a hash with last modified date and size for each FTP entry - this is data we have and could stick in the rule builder by default - but if we change that over time existing FTP rules will break. It would be much more sustainable to instead include the initial column generation information in the initial rules generated - so that each of these modalities start in reality with an empty table and the initial set of rules describe what metadata to pull initial columns from. This way if you save a set of rules it will include the initial column choices, and if they are pasted in at some later point where columns are picked differently - the rules will still work because you are replacing the initial column definitions. The initial rules implementation didn't have this concept of loading columns from metadata - but this was added to support loading existing identifiers as part of the "Apply Rules to Existing Collection" tool. This commit extends that idea to do the same thing (but with different columns) when loading data from HDAs, FTP, and data libraries. Commit: 3d6443b58bfa0200cf775b569c542be326476493 https://github.com/galaxyproject/galaxy/commit/3d6443b58bfa0200cf775b569c54… 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 client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Merge pull request #6134 from jmchilton/rule_fixes_8 Improve data initialization of rule builder for long term support. Compare: https://github.com/galaxyproject/galaxy/compare/076e1ddaecd4...3d6443b58bfa **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.

1 0

[galaxyproject/galaxy] e5ea32: More validation for rule builder.
by GitHub 15 May '18

15 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: e5ea32465a64fed1acfa63b7385272a6f9ccee15 https://github.com/galaxyproject/galaxy/commit/e5ea32465a64fed1acfa63b73852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- More validation for rule builder. - Require a URL or FTP column for raw pasted data. - Require list identifiers if creating collections. - Require name in more scenerios that require a name. Commit: 076e1ddaecd4f2744346c503b0108d8189f35bd1 https://github.com/galaxyproject/galaxy/commit/076e1ddaecd4f2744346c503b010… Author: Dannon <dannon.baker(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 #6136 from jmchilton/rule_fixes_9 [18.05] More validation for rule builder. Compare: https://github.com/galaxyproject/galaxy/compare/5c036bc26477...076e1ddaecd4 **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] 1940be: Add a script to prune ZFS snapshots from westvlete...
by GitHub 15 May '18

15 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1940bef1f7b65f380a5c9dd695b245ee2a34e5bd https://github.com/galaxyproject/infrastructure-playbook/commit/1940bef1f7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M common_roles A env/common/_inc_handlers.yml M env/galaxy/_inc_baseenv.yml A env/galaxy/_inc_handlers.yml A env/galaxy/files/system/prunesnaps A env/galaxy/files/westvleteren/prunesnaps.conf M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml Log Message: ----------- Add a script to prune ZFS snapshots from westvleteren. Testing, so not running from cron just yet **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] b77fa9: Clean cgroups every 5 minutes until I can figure o...
by GitHub 14 May '18

14 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b77fa95f1a7f946616cc4b9270abf0a0805d19bd https://github.com/galaxyproject/infrastructure-playbook/commit/b77fa95f1a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-14 (Mon, 14 May 2018) Changed paths: A env/tacc/files/system/cleancgroups.py M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Clean cgroups every 5 minutes until I can figure out why they're not being removed by slurm **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.

1 0