September 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 8054da: Update issues.rst
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8054da9fb4d858b7ff9dd461f8baa923fea99425 https://github.com/galaxyproject/galaxy/commit/8054da9fb4d858b7ff9dd461f8ba… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Update issues.rst Commit: 10703fac3a00a854bb3d4d548ab1dd22485199c5 https://github.com/galaxyproject/galaxy/commit/10703fac3a00a854bb3d4d548ab1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Merge pull request #2976 from martenson/issues-on-par-with-reality bring issues.rst on par with reality Compare: https://github.com/galaxyproject/galaxy/compare/aa70a97e1e57...10703fac3a00

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[galaxyproject/galaxy] d2ac5a: adding admin feature to allow user to turn on or o...
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d2ac5a001c1f2d17034622c5ad9298899b370ed3 https://github.com/galaxyproject/galaxy/commit/d2ac5a001c1f2d17034622c5ad92… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py M templates/webapps/galaxy/library/common/common.mako M tools/data_source/upload.py Log Message: ----------- adding admin feature to allow user to turn on or off line ending conversion Commit: bede2907b99951163b8cee69f79405abf4e44e1a https://github.com/galaxyproject/galaxy/commit/bede2907b99951163b8cee69f794… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M templates/webapps/galaxy/library/common/common.mako M tools/data_source/upload.py Log Message: ----------- added some changes to fix Commit: 8d8ea2158b5a7ba763985f369719f18c7b4230cc https://github.com/galaxyproject/galaxy/commit/8d8ea2158b5a7ba763985f369719… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- remove cProfile import Commit: c53585e8b5227e9d9f3536fa1434ae74acc0ef68 https://github.com/galaxyproject/galaxy/commit/c53585e8b5227e9d9f3536fa1434… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- added cProfile Commit: 66e3f8540f4dff918a90c2d02eca4a3f46f7fbdd https://github.com/galaxyproject/galaxy/commit/66e3f8540f4dff918a90c2d02eca… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- removed traces of cProfile and use Commit: bc1be68bb6f0eef840465dd2b578136d0094ae20 https://github.com/galaxyproject/galaxy/commit/bc1be68bb6f0eef840465dd2b578… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- added the extra blank line Commit: e85cd284d099af16329d6592b46dc3d6ce37dba4 https://github.com/galaxyproject/galaxy/commit/e85cd284d099af16329d6592b46d… Author: zipho <zipho.m(a)gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- fixed the line tabs Commit: aa70a97e1e570507121320d9f2370265fd25fca8 https://github.com/galaxyproject/galaxy/commit/aa70a97e1e570507121320d9f237… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py M templates/webapps/galaxy/library/common/common.mako Log Message: ----------- Merge pull request #2819 from SANBI-SA/upload_admin_line_endings Functionality to allow admins to switch on/off the line endings conversion on import Compare: https://github.com/galaxyproject/galaxy/compare/8ff8af7b248b...aa70a97e1e57

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[galaxyproject/galaxy] 7ecf93: Fix import order in containers.py (broken in cad40...
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ecf9377bf3780faa2bb93594cf41435a15ff40a https://github.com/galaxyproject/galaxy/commit/7ecf9377bf3780faa2bb93594cf4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix import order in containers.py (broken in cad4002efed5547ccc1f89a3a45d2d4b9b12f76d). Commit: 8ff8af7b248b79436113e03d3c01e2cc4cd2a88c https://github.com/galaxyproject/galaxy/commit/8ff8af7b248b79436113e03d3c01… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2975 from jmchilton/fix_import_order Fix import order in containers.py Compare: https://github.com/galaxyproject/galaxy/compare/002d974f8ada...8ff8af7b248b

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[galaxyproject/galaxy] cad400: Allow more rich container description in job_conf....
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cad4002efed5547ccc1f89a3a45d2d4b9b12f76d https://github.com/galaxyproject/galaxy/commit/cad4002efed5547ccc1f89a3a45d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Allow more rich container description in job_conf.xml. Commit: 6466ffe31e250575cc4ca278b0730ba7f1207e0d https://github.com/galaxyproject/galaxy/commit/6466ffe31e250575cc4ca278b073… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Allow more configurability in container descriptions. <container> descriptions (in job_conf.xml or in tool files) can now specify a few more options - including if Galaxy should perform tool dependency resolution (using the resolve_dependencies attribute - defaults to false) and job script shell (defaults to /bin/sh - but for containers with bash this should be overridden and set to /bin/bash). This should enable use cases such as that outlined in #2764. Commit: 002d974f8adae4cfc52c434c46c4966ac90918bd https://github.com/galaxyproject/galaxy/commit/002d974f8adae4cfc52c434c46c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Merge pull request #2790 from jmchilton/docker_container_xml More configurability for containerized jobs Compare: https://github.com/galaxyproject/galaxy/compare/0df6ff9f2d7d...002d974f8ada

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[galaxyproject/usegalaxy-playbook] bdc76b: Updated integrated tool panel for Trinity on Main
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bdc76b2c117d48fe0ce1af06c45c9ad738f3e220 https://github.com/galaxyproject/usegalaxy-playbook/commit/bdc76b2c117d48fe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- Updated integrated tool panel for Trinity on Main Commit: 1de0da3101cb79a84451e43a44d638bddd5c47df https://github.com/galaxyproject/usegalaxy-playbook/commit/1de0da3101cb79a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M production/host_vars/br005.bridges.psc.edu.yml Log Message: ----------- Install dependency_resolvers_conf.xml on Bridges for Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/29f7ff12d0cb...…

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[galaxyproject/usegalaxy-playbook] 18340f: Update Main
by GitHub 27 Sep '16

27 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 18340f9502b4ce066d59de8cf388ecac1cf02a14 https://github.com/galaxyproject/usegalaxy-playbook/commit/18340f9502b4ce06… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main Commit: 29f7ff12d0cb80f1a117a428ef4e2efaa00e455a https://github.com/galaxyproject/usegalaxy-playbook/commit/29f7ff12d0cb80f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-27 (Tue, 27 Sep 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Cut 'n paste error from Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/4a8302799db4...…

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[galaxyproject/usegalaxy-playbook] 4a8302: Apparently I never committed the galaxy_url change...
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4a8302799db46e7630c5ffdd4c8ce33c4503e47c https://github.com/galaxyproject/usegalaxy-playbook/commit/4a8302799db46e76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Apparently I never committed the galaxy_url changes? Also, change Bridges native spec for updated dynamic rule

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[galaxyproject/usegalaxy-playbook] 07e54c: Enable iobio on Test
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 07e54c5c412ef28cc589e18178854fa4bfc8e911 https://github.com/galaxyproject/usegalaxy-playbook/commit/07e54c5c412ef28c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M files/galaxy/test.galaxyproject.org/config/tool_data_table_conf.xml M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 Log Message: ----------- Enable iobio on Test

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[galaxyproject/galaxy] 8b452c: Remove invalid attribute metadata_name from param ...
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b452c9dc3dca9c4ba8804e0a3e6edd8d06946c0 https://github.com/galaxyproject/galaxy/commit/8b452c9dc3dca9c4ba8804e0a3e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Remove invalid attribute metadata_name from param examples in XSD docs. Pointed out by @peterjc in https://github.com/galaxyproject/tools-iuc/pull/964#issuecomment-249632638. Commit: 0df6ff9f2d7d841b322ee690a84ec8baa822b336 https://github.com/galaxyproject/galaxy/commit/0df6ff9f2d7d841b322ee690a84e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #2974 from jmchilton/schema_fix_0 Remove invalid attribute metadata_name from param examples in XSD docs. Compare: https://github.com/galaxyproject/galaxy/compare/051d2b285487...0df6ff9f2d7d

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[galaxyproject/galaxy] 750cb7: encourage bug reporting in tool schema
by GitHub 26 Sep '16

26 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 750cb7c5843fee4c82f7b028fa59d718a0629927 https://github.com/galaxyproject/galaxy/commit/750cb7c5843fee4c82f7b028fa59… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M doc/schema_template.md Log Message: ----------- encourage bug reporting in tool schema Commit: 051d2b285487fb99a065448b20f69f0d82d3a100 https://github.com/galaxyproject/galaxy/commit/051d2b285487fb99a065448b20f6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M doc/schema_template.md Log Message: ----------- Merge pull request #2972 from martenson/tool-schema-report encourage bug reporting in tool schema document Compare: https://github.com/galaxyproject/galaxy/compare/780473a751ae...051d2b285487

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