- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 64b461: Update Platform LSF to Spectrum LSF
by Nicola Soranzo 08 Mar '19

08 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 64b461eac80d9e8ee8fc62a48db541f7ead1754f https://github.com/galaxyproject/galaxy/commit/64b461eac80d9e8ee8fc62a48db5… Author: Peter Selten <peter(a)pselten.info> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Update Platform LSF to Spectrum LSF Commit: 844839f028273d213573378d8d7b90b8e6901585 https://github.com/galaxyproject/galaxy/commit/844839f028273d213573378d8d7b… Author: Peter Selten <peter(a)pselten.info> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Update CLIJobRunner to ShellJobRunner according to #7433 Commit: 05d1cdcd6db18813ffbc1a5e19b47e40a32edda0 https://github.com/galaxyproject/galaxy/commit/05d1cdcd6db18813ffbc1a5e19b4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #7486 from selten/doc-LSF-upgrade Update Platform LSF to Spectrum LSF Compare: https://github.com/galaxyproject/galaxy/compare/c714b6e66500...05d1cdcd6db1

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[galaxyproject/infrastructure-playbook] d84727: Use X-Forwarded-Hosts to fix FILTER_VHOST
by Nate Coraor 08 Mar '19

08 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d847272935ace7d566fa2b0e805de32b0c3ce29a https://github.com/galaxyproject/infrastructure-playbook/commit/d847272935a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M env/mailman/group_vars/listservers/vars.yml Log Message: ----------- Use X-Forwarded-Hosts to fix FILTER_VHOST Commit: d43fefe0c51923a4711c638b5a9e0b66f5bc3c0c https://github.com/galaxyproject/infrastructure-playbook/commit/d43fefe0c51… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M env/galaxy/inventory M env/galaxy/playbook.yml M env/galaxy/templates/nginx/lists.j2 M env/mailman/TODO.txt M env/mailman/group_vars/listservers/vars.yml M env/mailman/listservers.yml M env/mailman/templates/nginx/mailman_ssl.j2 M roles/postfix/templates/main.cf.j2 Log Message: ----------- Mailman 3 is live Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/a950a46bf8…

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[galaxyproject/galaxy] 19816f: Add a validator that ensures one metadata is betwe...
by Martin Cech 07 Mar '19

07 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19816f2c25777805bbb3bb7406f36a1fe4fbdb52 https://github.com/galaxyproject/galaxy/commit/19816f2c25777805bbb3bb7406f3… Author: Fabien Mareuil <fmareuil(a)pasteur.fr> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Add a validator that ensures one metadata is between min and max values Commit: 1ef8e0afe1e743ad514e176490e709b63ce10620 https://github.com/galaxyproject/galaxy/commit/1ef8e0afe1e743ad514e176490e7… Author: fmareuil <fmareuil(a)pasteur.fr> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Update validation.py pylint correction Commit: f6bc62dbd26a4633f153ee13ea34f9b50f0548de https://github.com/galaxyproject/galaxy/commit/f6bc62dbd26a4633f153ee13ea34… Author: fmareuil <fmareuil(a)pasteur.fr> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Update validation.py tool_data_table_conf is not required Commit: 531f4f8d9fd0977f3958afb919f8abba40fe9f8a https://github.com/galaxyproject/galaxy/commit/531f4f8d9fd0977f3958afb919f8… Author: fmareuil <fmareuil(a)pasteur.fr> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Update validation.py Bug fix: raise an error if metadata is missing Commit: 05481d57a13fd5e791ae314a1af21bf1aab002a4 https://github.com/galaxyproject/galaxy/commit/05481d57a13fd5e791ae314a1af2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_metadata_in_range.xml Log Message: ----------- Add tool test for metadata_in_range Reduce copy and paste by inheriting from InRangeValidator and add new validator to xsd schema. Commit: f0066ca19414ee625eb4a11a5b4901ce0994a4d7 https://github.com/galaxyproject/galaxy/commit/f0066ca19414ee625eb4a11a5b49… Author: fmareuil <fmareuil(a)pasteur.fr> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_metadata_in_range.xml Log Message: ----------- Merge pull request #1 from mvdbeek/fmareuil-dev Add tool test for metadata_in_range Commit: 8212f5d57d1227ee9bbfd85f12c141705abcb961 https://github.com/galaxyproject/galaxy/commit/8212f5d57d1227ee9bbfd85f12c1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_metadata_in_range.xml Log Message: ----------- Fix test tool label and tool xsd Commit: b8c5ee37680f166246d247bbf06e1800e4d8310b https://github.com/galaxyproject/galaxy/commit/b8c5ee37680f166246d247bbf06e… Author: fmareuil <fmareuil(a)pasteur.fr> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_metadata_in_range.xml Log Message: ----------- Merge pull request #2 from mvdbeek/fmareuil-dev Fix test tool label and tool xsd Commit: c714b6e665003cc693f6dcc844032fd1c58d851e https://github.com/galaxyproject/galaxy/commit/c714b6e665003cc693f6dcc84403… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_metadata_in_range.xml Log Message: ----------- Merge pull request #7288 from fmareuil/dev Add a validator that ensures one metadata is between min and max values Compare: https://github.com/galaxyproject/galaxy/compare/192a091d1655...c714b6e66500

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[galaxyproject/galaxy] 4bcd46: Show an exception message if authentication has fa...
by John Chilton 07 Mar '19

07 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4bcd46acf55897c2b56b470b1dddcd59f756093f https://github.com/galaxyproject/galaxy/commit/4bcd46acf55897c2b56b470b1ddd… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Show an exception message if authentication has failed. Commit: 56b36cb4b51432796ac32d3819795a66b1bd8af4 https://github.com/galaxyproject/galaxy/commit/56b36cb4b51432796ac32d381979… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Correctly report the unrecognized provider name. Commit: 192a091d16552fae610eef9df8f821afb04a6594 https://github.com/galaxyproject/galaxy/commit/192a091d16552fae610eef9df8f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Merge pull request #7442 from VJalili/upgrade_psa Inform users if an exception has happened authenticating via OIDC Compare: https://github.com/galaxyproject/galaxy/compare/a10813a4f8c8...192a091d1655

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[galaxyproject/galaxy] b089cf: Test data for microarrays data types, Gal and Gpr
by Marius van den Beek 07 Mar '19

07 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b089cfeab52b31bbdff83fd4facf079208fed8f6 https://github.com/galaxyproject/galaxy/commit/b089cfeab52b31bbdff83fd4facf… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: A lib/galaxy/datatypes/test/test.gal A lib/galaxy/datatypes/test/test.gpr Log Message: ----------- Test data for microarrays data types, Gal and Gpr Commit: 3722b37a4f71e1a84d416b6a785eb38774a76e88 https://github.com/galaxyproject/galaxy/commit/3722b37a4f71e1a84d416b6a785e… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: A lib/galaxy/datatypes/microarrays.py Log Message: ----------- Added Gpr and Gal classes defintion. Commit: e080098656c5d45189a8f2f2a4f772dc7a23b220 https://github.com/galaxyproject/galaxy/commit/e080098656c5d45189a8f2f2a4f7… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Added data types Gpr and Gal Gpr and Gal extensions and sniffers Commit: 739be4fdd05df2e19134095cfbdc5fda80ba7494 https://github.com/galaxyproject/galaxy/commit/739be4fdd05df2e19134095cfbdc… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Update lib/galaxy/datatypes/microarrays.py Co-Authored-By: bensellak <bensellak(a)ensat.ac.ma> Commit: 2e03231077321103b4d45495c96a6e98a5507039 https://github.com/galaxyproject/galaxy/commit/2e03231077321103b4d45495c96a… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Update microarrays.py Commit: c6d1e5f328f3ca2589dc53869858208a302fe7e9 https://github.com/galaxyproject/galaxy/commit/c6d1e5f328f3ca2589dc53869858… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Fix ``get_file_peek`` import Commit: 55edbde1393e7c0caf45d3edd6c4cc202b97af9d https://github.com/galaxyproject/galaxy/commit/55edbde1393e7c0caf45d3edd6c4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Remove ``get_n_first_lines`` function Commit: b3ffbc84e376c1abcad32254310323b131e0e5c9 https://github.com/galaxyproject/galaxy/commit/b3ffbc84e376c1abcad322543103… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py M lib/galaxy/datatypes/molecules.py Log Message: ----------- Reuse ``count_special_lines`` from ``galaxy.datatypes.util.generic_util`` Commit: eb50086040a358acddeceab14998f11707544d99 https://github.com/galaxyproject/galaxy/commit/eb50086040a358acddeceab14998… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix typo Commit: 546e728620b7aa45e7248f98255cf4ee6898a850 https://github.com/galaxyproject/galaxy/commit/546e728620b7aa45e7248f98255c… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Trying to solve the peek issue Commit: aa5a31d7c60cf04b4eee737728cd6dca4f7469c0 https://github.com/galaxyproject/galaxy/commit/aa5a31d7c60cf04b4eee737728cd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/datatypes/test/test.gal Log Message: ----------- dos2unix test.gal Commit: bacd3eeccf974d4f70b5b22db4d17eb7d4418789 https://github.com/galaxyproject/galaxy/commit/bacd3eeccf974d4f70b5b22db4d1… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/datatypes/test/test.gpr Log Message: ----------- dos2unix test.gpr Commit: f5ee004ea57e21e7e292a5a42b73374aebd39afd https://github.com/galaxyproject/galaxy/commit/f5ee004ea57e21e7e292a5a42b73… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/datatypes/test/test.gpr Log Message: ----------- iconv -f ISO-8859-1 -t UTF-8 test.gpr Commit: d3a7f383d9c32646419f378d699207521a6bc348 https://github.com/galaxyproject/galaxy/commit/d3a7f383d9c32646419f378d6992… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Modified classes definition, metadata and sniffing Commit: f47048bb9cb4af458a00f66389292f552a243aaf https://github.com/galaxyproject/galaxy/commit/f47048bb9cb4af458a00f6638929… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Update microarrays.py Commit: 7f25bb7874b8a5a3c83e99147189600c15e781db https://github.com/galaxyproject/galaxy/commit/7f25bb7874b8a5a3c83e99147189… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Add files via upload Commit: cfb854f6c7dc30297a509c5e39fd1387834a0f88 https://github.com/galaxyproject/galaxy/commit/cfb854f6c7dc30297a509c5e39fd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Use ``sniff_prefix()`` Commit: d140178dc67fd937e2006643f2a7309454ce0b7b https://github.com/galaxyproject/galaxy/commit/d140178dc67fd937e2006643f2a7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Use ``enumerate()`` Commit: 9621900512b4178f116d3f0b7ed06f6504b1980d https://github.com/galaxyproject/galaxy/commit/9621900512b4178f116d3f0b7ed0… Author: bensellak <bensellak(a)ensat.ac.ma> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Update microarrays.py Commit: 5f738d95038ccb47ec533b033ba333069b28a6bb https://github.com/galaxyproject/galaxy/commit/5f738d95038ccb47ec533b033ba3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- Forgot to remove increment to count Introduced in commit d140178dc67fd937e2006643f2a7309454ce0b7b Commit: cf2f192d1b1a5d9b5883c65a433776d93934635d https://github.com/galaxyproject/galaxy/commit/cf2f192d1b1a5d9b5883c65a4337… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/datatypes/microarrays.py Log Message: ----------- No need to iterate Commit: a10813a4f8c8c69c84b4d58bd0fb57d124394c97 https://github.com/galaxyproject/galaxy/commit/a10813a4f8c8c69c84b4d58bd0fb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/microarrays.py M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/test.gal A lib/galaxy/datatypes/test/test.gpr Log Message: ----------- Merge pull request #7457 from bensellak/dev Adding microarrays data types Gpr and Gal Compare: https://github.com/galaxyproject/galaxy/compare/3649c01a0c7f...a10813a4f8c8

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[galaxyproject/galaxy] 9d0cf4: added option to pass in individual globs to unit t...
by Dannon 07 Mar '19

07 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d0cf40fe8989364c47ad75ef8c5631d2bc0887f https://github.com/galaxyproject/galaxy/commit/9d0cf40fe8989364c47ad75ef8c5… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M client/karma/karma.config.mocha.js Log Message: ----------- added option to pass in individual globs to unit test watcher Commit: 8a0b1343e55f3be3b6b17315b9ee5a8af21e7fd6 https://github.com/galaxyproject/galaxy/commit/8a0b1343e55f3be3b6b17315b9ee… Author: Mason <nerdinacan(a)gmail.com> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M client/karma/karma.config.mocha.js Log Message: ----------- Reconfigured args to jive with galaxy arg style Commit: 3649c01a0c7f8ebbdedbb052252157b66a419920 https://github.com/galaxyproject/galaxy/commit/3649c01a0c7f8ebbdedbb0522521… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M client/karma/karma.config.mocha.js Log Message: ----------- Merge pull request #7477 from Nerdinacan/watch_individual_karma_tests added option to pass in individual globs to unit test watcher Compare: https://github.com/galaxyproject/galaxy/compare/8bc23e03e020...3649c01a0c7f

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[galaxyproject/galaxy] 53286c: Refactor output discovery toward cohesiveness in j...
by Marius van den Beek 06 Mar '19

06 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 53286c51dcd0aff38ade2f33d1aa8252953ddfb5 https://github.com/galaxyproject/galaxy/commit/53286c51dcd0aff38ade2f33d1aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Refactor output discovery toward cohesiveness in job wrapper. Commit: 0967412e3f66b5d89307a7e98849d4b3445f40d9 https://github.com/galaxyproject/galaxy/commit/0967412e3f66b5d89307a7e98849… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Refactor output discovery toward cohesiveness in Tool class. Commit: df0e58ba11154cad2629ed252d84a151b6be0995 https://github.com/galaxyproject/galaxy/commit/df0e58ba11154cad2629ed252d84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Relocate job param code for clarity. Commit: 2841a3dc260753ede5ed6aeae3971f3fa6b45b77 https://github.com/galaxyproject/galaxy/commit/2841a3dc260753ede5ed6aeae397… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Refactor output_collect to use app less. Commit: 3077895b22cfcedfce272c07ef8a8db3794fa26c https://github.com/galaxyproject/galaxy/commit/3077895b22cfcedfce272c07ef8a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Relocate dynamic output metadata source code for clarity. Commit: 8bc23e03e020a4199e9fa1c405b5f2fd50c39f09 https://github.com/galaxyproject/galaxy/commit/8bc23e03e020a4199e9fa1c405b5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #7471 from jmchilton/model_free_job_refactor_0 Collected Refactoring of Job Output Handling Code Compare: https://github.com/galaxyproject/galaxy/compare/492ee286969e...8bc23e03e020

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[galaxyproject/galaxy] 557407: correct virtualenv download with no wget/curl
by Dannon 06 Mar '19

06 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 557407c384d065a6c37e8f4c8466d6a53d9fbacd https://github.com/galaxyproject/galaxy/commit/557407c384d065a6c37e8f4c8466… Author: Hervé Ménager <herve.menager(a)gmail.com> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- correct virtualenv download with no wget/curl the embedded python code needs a small correction to work in the no curl/wget available case. Commit: 492ee286969e7fa4d716945a8ffc06181b310e5f https://github.com/galaxyproject/galaxy/commit/492ee286969e7fa4d716945a8ffc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-06 (Wed, 06 Mar 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7476 from hmenager/patch-1 correct virtualenv download with no wget/curl Compare: https://github.com/galaxyproject/galaxy/compare/67aac7b2c598...492ee286969e

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[galaxyproject/galaxy] 9d4f85: Fix workflow_building_mode typo
by Martin Cech 05 Mar '19

05 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d4f857378a782d0782ef7cd7584f33d1a38686b https://github.com/galaxyproject/galaxy/commit/9d4f857378a782d0782ef7cd7584… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix workflow_building_mode typo Commit: 05dbbe5b6eb427e03f49ab5f04f6d5188db6fb36 https://github.com/galaxyproject/galaxy/commit/05dbbe5b6eb427e03f49ab5f04f6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Use correct tools in skip_without_tool decorator Commit: 67aac7b2c598fba7bd559a7fe95a2b66d3f0a483 https://github.com/galaxyproject/galaxy/commit/67aac7b2c598fba7bd559a7fe95a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #7472 from mvdbeek/fix_workflow_building_typo Fix workflow building typo Compare: https://github.com/galaxyproject/galaxy/compare/0a37bb0da0c2...67aac7b2c598

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[galaxyproject/infrastructure-playbook] 5dc8b5: Mount Postorius at / and Hyperkitty at /archives
by Nate Coraor 05 Mar '19

05 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5dc8b56bad0eef2cdd1251125482dc6c612f2534 https://github.com/galaxyproject/infrastructure-playbook/commit/5dc8b56bad0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M env/mailman/group_vars/listservers/vars.yml Log Message: ----------- Mount Postorius at / and Hyperkitty at /archives Commit: a950a46bf881324a8519ea5742f5e88b94768f5e https://github.com/galaxyproject/infrastructure-playbook/commit/a950a46bf88… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M env/mailman/group_vars/listservers/vars.yml M env/mailman/listservers.yml Log Message: ----------- Use xapian for Hyperkitty indexes Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/6ec3e53029…

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