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

[galaxyproject/infrastructure-playbook] bc9ad6: New Docker CA and server certs
by GitHub 21 Mar '18

21 Mar '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: bc9ad65d929be306b8429e15fba596073bce3610 https://github.com/galaxyproject/infrastructure-playbook/commit/bc9ad65d929… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: A env/common/files/ssl/athena.galaxyproject.org_cert.pem M env/common/files/ssl/docker/ca-key.pem M env/common/files/ssl/docker/ca.pem M env/common/files/ssl/docker/ca.srl R env/common/files/ssl/docker/client.pem R env/common/files/ssl/docker/client_privatekey.yml M env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem M env/common/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey… M env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem M env/common/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek… R env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p… A env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server.pem M env/common/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat… A env/galaxy/files/ssl R env/galaxy/files/ssl/athena.galaxyproject.org_cert.pem R env/galaxy/files/ssl/wildcard_cert.pem M env/galaxy/group_vars/dockersslservers/vars.yml M env/galaxy/inventory Log Message: ----------- New Docker CA and server certs

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[galaxyproject/infrastructure-playbook] b763fb: Stratum 0 upgrades I forgot to commit
by GitHub 21 Mar '18

21 Mar '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b763fb25cfc72d65ff9207293e03410dec3642eb https://github.com/galaxyproject/infrastructure-playbook/commit/b763fb25cfc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M env/galaxy/group_vars/cvmfsstratum0servers.yml M env/galaxy/host_vars/cvmfs0-tacc0.galaxyproject.org/vars.yml M roles/cvmfs/tasks/stratum0.yml Log Message: ----------- Stratum 0 upgrades I forgot to commit

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[galaxyproject/galaxy] c74868: Tool versions should follow PEP 440
by GitHub 21 Mar '18

21 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c74868a1e670a28b934807c5a2c161e431dc0f88 https://github.com/galaxyproject/galaxy/commit/c74868a1e670a28b934807c5a2c1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Tool versions should follow PEP 440 to ensure a correct tool lineage. Commit: 0369a4028d1732e727ae9e90adf4668a3b3b3ddd https://github.com/galaxyproject/galaxy/commit/0369a4028d1732e727ae9e90adf4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #5746 from nsoranzo/pep440 Tool versions should follow PEP 440 Compare: https://github.com/galaxyproject/galaxy/compare/890e6327e8dd...0369a4028d17

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[galaxyproject/galaxy] c0ec91: Remove unused function
by GitHub 21 Mar '18

21 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0ec919d2869e3ea700a285b7eda4adab2f7497b https://github.com/galaxyproject/galaxy/commit/c0ec919d2869e3ea700a285b7eda… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Remove unused function Last use removed in commit 87db3952d38df4bc417dea2030a8ff5cdc93395f . Commit: 597b437b71c2a4f55e255bc5c6fd1a59339bb77d https://github.com/galaxyproject/galaxy/commit/597b437b71c2a4f55e255bc5c6fd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Simplify unicodify().encode() to smart_str() Belated follow-up to https://github.com/galaxyproject/galaxy/pull/1905 Commit: 03f5f5310ed75c912b93baa4da6cc0d858512164 https://github.com/galaxyproject/galaxy/commit/03f5f5310ed75c912b93baa4da6c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/job_conf.xml.sample_advanced M doc/source/admin/nginx.md M doc/source/admin/scaling.md M test/api/test_workflows.py Log Message: ----------- Fix typos Commit: 2921af9bda5fff72f5764cef37e7476b53f136d5 https://github.com/galaxyproject/galaxy/commit/2921af9bda5fff72f5764cef37e7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Allow bool type in UWSGI_OPTIONS dict Commit: 890e6327e8ddf85702fc1c1c2990779813396885 https://github.com/galaxyproject/galaxy/commit/890e6327e8ddf85702fc1c1c2990… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/job_conf.xml.sample_advanced M doc/source/admin/nginx.md M doc/source/admin/scaling.md M lib/galaxy/datatypes/sniff.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/remote_files.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5747 from nsoranzo/typos_refactors Typo fixes and small refactors Compare: https://github.com/galaxyproject/galaxy/compare/0823d0e554fb...890e6327e8dd

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[galaxyproject/galaxy] 64deb6: Fix broken API test.
by GitHub 21 Mar '18

21 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 64deb6311712c0d28edef6ce689d0ce184ccb226 https://github.com/galaxyproject/galaxy/commit/64deb6311712c0d28edef6ce689d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M test/api/test_libraries.py Log Message: ----------- Fix broken API test. I think the URLs changed so checksum computation is failing. Commit: 0823d0e554fbef8e7667f1efea8c78864d3318d7 https://github.com/galaxyproject/galaxy/commit/0823d0e554fbef8e7667f1efea8c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M test/api/test_libraries.py Log Message: ----------- Merge pull request #5740 from jmchilton/bagit_example_broken Fix broken bagit API test. Compare: https://github.com/galaxyproject/galaxy/compare/d1489ca57ce8...0823d0e554fb

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[galaxyproject/galaxy] 05176d: Restructure and mark as flakey problematic library...
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 05176dabbe30ba9565c4f5a6865c012aada9e047 https://github.com/galaxyproject/galaxy/commit/05176dabbe30ba9565c4f5a6865c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_library_to_collections.py Log Message: ----------- Restructure and mark as flakey problematic library collection Selenium test. Needs to be restructured for flakey to work, several other PRs attempted to address or clarify this but have failed. Commit: d1489ca57ce80b7fc85f59cf2158cc041898c101 https://github.com/galaxyproject/galaxy/commit/d1489ca57ce80b7fc85f59cf2158… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M test/selenium_tests/test_library_to_collections.py Log Message: ----------- Merge pull request #5714 from jmchilton/defeated_by_selenium Restructure and mark as flakey problematic library collection Selenium test. Compare: https://github.com/galaxyproject/galaxy/compare/40e87162597d...d1489ca57ce8

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[galaxyproject/galaxy] 5ed6d5: Hack around bug in uploader where it sometimes pos...
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ed6d50d476fe36e90e790b6214b3df1fac057ed https://github.com/galaxyproject/galaxy/commit/5ed6d50d476fe36e90e790b6214b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Hack around bug in uploader where it sometimes posts with empty "file_type". Galaxy really needs this to be "auto". Seems to happen in automated testing, maybe because things move faster and something hasn't had time to reset? xref https://github.com/galaxyproject/galaxy/issues/5169 Commit: 40e87162597df53b8210f5cb789721633018f370 https://github.com/galaxyproject/galaxy/commit/40e87162597df53b8210f5cb7897… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Merge pull request #5692 from jmchilton/selenium_fixes_35 Hack to fix bug in uploader where it sometimes posts with empty "file_type". Compare: https://github.com/galaxyproject/galaxy/compare/240d72bdd57f...40e87162597d

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[galaxyproject/galaxy] f75463: Remove extract_genomic_dna tool from sample.
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f75463e5cfae4c3a288501836e88d72c2f662142 https://github.com/galaxyproject/galaxy/commit/f75463e5cfae4c3a288501836e88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Remove extract_genomic_dna tool from sample. It has serious issues and a better version from the IUC is available at https://toolshed.g2.bx.psu.edu/repository?repository_id=5e1b70f8c4a31a72&ch…. Alternative to https://github.com/galaxyproject/galaxy/pull/5618 until the tool is migrated out of Galaxy in some fashion. Keeping it in the code but not in the sample for now means existing deployers who want to keep it get to without making any changes but it prevents new deployers from having to figure out it is broken and a better version is available. Commit: 240d72bdd57fe46664d9e045ff0a688c6fc64e2a https://github.com/galaxyproject/galaxy/commit/240d72bdd57fe46664d9e045ff0a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Merge pull request #5741 from jmchilton/extract_genome_dna_remove_from_sample Remove extract_genomic_dna tool from tool sample. Compare: https://github.com/galaxyproject/galaxy/compare/6422955a22d9...240d72bdd57f

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[galaxyproject/usegalaxy-playbook] aa0b86: Updated Main
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aa0b86f0c5d31ee214b69757a3869be9220a7866 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa0b86f0c5d31ee2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/cvmfsstratum0servers.yml Log Message: ----------- Updated Main

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[galaxyproject/galaxy] cf4936: Minor cleanup in galaxy.tools.actions
by GitHub 20 Mar '18

20 Mar '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: cf4936b3d480011a4638a393776dd5ec94f11ae4 https://github.com/galaxyproject/galaxy/commit/cf4936b3d480011a4638a393776d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Minor cleanup in galaxy.tools.actions Commit: 513b6a5d65676a2f03d6c4580d16e053d8fe6aaf https://github.com/galaxyproject/galaxy/commit/513b6a5d65676a2f03d6c4580d16… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix a few mutable default params in workflow/run_request. Commit: cb5e81b6a1209ef89dd7edc9bdd870c8953a96a5 https://github.com/galaxyproject/galaxy/commit/cb5e81b6a1209ef89dd7edc9bdd8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- replace incorrect list add syntax Commit: 332d79eb72c4bae90c911707d4db9285556c59b1 https://github.com/galaxyproject/galaxy/commit/332d79eb72c4bae90c911707d4db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix 'uknown' typo in model exceptions Commit: 6b9afb6b360108b194c03ca262a20013b444ece9 https://github.com/galaxyproject/galaxy/commit/6b9afb6b360108b194c03ca262a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- rmeove overly zealous syntax fix thanks to dannon Commit: 04404f915c70b90a9d4a56dbeb030748163dce16 https://github.com/galaxyproject/galaxy/commit/04404f915c70b90a9d4a56dbeb03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Support re-execution of immediate PJAs when requing jobs Commit: b685b53d13b9fa91c4abcb631fc3cd5c68d5d9c4 https://github.com/galaxyproject/galaxy/commit/b685b53d13b9fa91c4abcb631fc3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Ship context along with PJA execution when remapping workflow immediate actions Commit: 6a7fb23f11e26b3761cb71128a4c5e0ac605d818 https://github.com/galaxyproject/galaxy/commit/6a7fb23f11e26b3761cb71128a4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Instead of denoting unused var from items(), just use values() Commit: f1dd060d73ccb369aafb1a56e902e4d4faf6dd64 https://github.com/galaxyproject/galaxy/commit/f1dd060d73ccb369aafb1a56e902… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test rename PJA when resuming a failed job Commit: 8dfc1523d31e56a3e632e0d490d08c15722764d5 https://github.com/galaxyproject/galaxy/commit/8dfc1523d31e56a3e632e0d490d0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #26 from mvdbeek/workflow-resume-pjas Test rename PJA when resuming a failed job Commit: 5cf3d44a6ad5f53c3f263ac2a28484686e44ea6a https://github.com/galaxyproject/galaxy/commit/5cf3d44a6ad5f53c3f263ac2a284… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- Merge pull request #5676 from martenson/fix-library-add [18.01] replace incorrect list add syntax Commit: 040bf5ba77562cc20b822b2068860c2bf6c0399e https://github.com/galaxyproject/galaxy/commit/040bf5ba77562cc20b822b206886… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5678 from dannon/workflow-resume-pjas [18.01] Support re-execution of immediate PJAs when re-queing jobs Commit: 31cb24e4229767425a72d6981bcb359b15792254 https://github.com/galaxyproject/galaxy/commit/31cb24e4229767425a72d6981bcb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-genomespace.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/ui/loading-indicator.js.map M static/maps/utils/config.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/ui/loading-indicator.js M static/scripts/utils/config.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css Log Message: ----------- add built client with maps for 18.01 tagging Commit: 0182d8d0bec3cf78401434e5c07b012eabcda7e3 https://github.com/galaxyproject/galaxy/commit/0182d8d0bec3cf78401434e5c07b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.01 Commit: 73e61f5fdc4011d838ff5862ed3713fdca48762e https://github.com/galaxyproject/galaxy/commit/73e61f5fdc4011d838ff5862ed37… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- add security announcement to the rn Commit: ebb7be8d0ec3944eb945f5cc6e57087328e69d5e https://github.com/galaxyproject/galaxy/commit/ebb7be8d0ec3944eb945f5cc6e57… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge pull request #5688 from martenson/security-rn [18.01] backport add security announcement to the release notes Commit: be02063c3fbec79a7e146ef87dbc6e99c80e7754 https://github.com/galaxyproject/galaxy/commit/be02063c3fbec79a7e146ef87dbc… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Set the role type to SYSTEM for auto generated roles, which is similar to the default behavior Commit: c58ca749c26bbb3c4ca8750f2c37fd1bb6bd7999 https://github.com/galaxyproject/galaxy/commit/c58ca749c26bbb3c4ca8750f2c37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #5709 from scholtalbers/fix/default_ldap_role_type [18.01] Fix/default role type on auto created roles Commit: d5d1e4b80d84ebafccfd1e8cc642dbcd1f020d55 https://github.com/galaxyproject/galaxy/commit/d5d1e4b80d84ebafccfd1e8cc642… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Clarfify that nginx-extras needs to be install for the upload_store directive to work Commit: 127d7b8c3c854db7a28c761aee0c3f2d2e211a6e https://github.com/galaxyproject/galaxy/commit/127d7b8c3c854db7a28c761aee0c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/admin/nginx.md Log Message: ----------- Merge pull request #5717 from mvdbeek/nginx_doc_update [18.01] Clarify that nginx-extras needs to be install for the upload_store d… Commit: 3b87dac78028846a803e33ae13199535c70f567d https://github.com/galaxyproject/galaxy/commit/3b87dac78028846a803e33ae1319… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Add Galaxy `lib` directory to Python path for 2 scripts Also fix check introduced in commit 0763cab37a818a9252a01a7aa387b1fecc07d17e . Fix https://github.com/galaxyproject/galaxy/issues/5722 . Commit: ef45ae3752a4ea4da73719e2917a064c8e239ab3 https://github.com/galaxyproject/galaxy/commit/ef45ae3752a4ea4da73719e2917a… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Upgrade clone failure logging to error When a failed clone logs as log.debug() this is invisible to a production Galaxy admin. This change upgrades the logging to 'log.error()'. Commit: 5dcd9ed0255c4c0bcf41059c79bfb912337ed009 https://github.com/galaxyproject/galaxy/commit/5dcd9ed0255c4c0bcf41059c79bf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Merge pull request #5725 from nsoranzo/release_17.09_fix_cleanup_scripts [17.09] Add Galaxy `lib` directory to Python path for 2 scripts Commit: 50035b184e0ceba61f21f223e5f701710dd86d19 https://github.com/galaxyproject/galaxy/commit/50035b184e0ceba61f21f223e5f7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- improve update commands in RN, clarify uwsgi config changes Commit: 74d0bcb353b4824d4d4af9ffe6bd909924feca62 https://github.com/galaxyproject/galaxy/commit/74d0bcb353b4824d4d4af9ffe6bd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 924eecc67a3155578aea6a484d9bfd86d0cc5aba https://github.com/galaxyproject/galaxy/commit/924eecc67a3155578aea6a484d9b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Add missing `.` Commit: 3699e9e4919dcb727af3ff0e7457794642973dfa https://github.com/galaxyproject/galaxy/commit/3699e9e4919dcb727af3ff0e7457… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- re-add the motivation for uwsgi switch Commit: 240f14d62fb6bdbf02f51ff1af19602494560880 https://github.com/galaxyproject/galaxy/commit/240f14d62fb6bdbf02f51ff1af19… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst Log Message: ----------- Merge pull request #5730 from martenson/bootstrap [18.01] improve update commands in RN, clarify uwsgi config changes Commit: a73a1d6250373cd1e6bb1255052ee7cb541e4569 https://github.com/galaxyproject/galaxy/commit/a73a1d6250373cd1e6bb1255052e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #5728 from mvdbeek/backport_logging_level_change [18.01] Backport 5724: upgrade clone failure logging to error Commit: 7c962975750c9747b12413309ac0c546fe8a9046 https://github.com/galaxyproject/galaxy/commit/7c962975750c9747b12413309ac0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M doc/source/admin/nginx.md M doc/source/releases/18.01_announce.rst M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/version.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/hg_util.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-genomespace.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/ui/loading-indicator.js.map M static/maps/utils/config.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-genomespace.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/ui/loading-indicator.js M static/scripts/utils/config.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M static/style/blue/base.css M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/e12e773eddca...7c962975750c

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