galaxy-commits February 2019

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[galaxyproject/galaxy] c0dca7: Respect `section=False` parameter in `BaseToolBoxT...
by Marius van den Beek 05 Feb '19

05 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c0dca7a44cd12492ec34ad9c7cf2a7aa5ab0d116 https://github.com/galaxyproject/galaxy/commit/c0dca7a44cd12492ec34ad9c7cf2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Respect `section=False` parameter in `BaseToolBoxTestCase._setup_two_versions_in_config()` Broken in commit fd1c34b4c9fec55286c3d33e2802062ef393de82 Commit: 87d4904189e42b9263bea70a321bf80ae4549a93 https://github.com/galaxyproject/galaxy/commit/87d4904189e42b9263bea70a321b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Remove spurious quote Commit: ab03de44e86a376a4c7d98dad9b683992327aa32 https://github.com/galaxyproject/galaxy/commit/ab03de44e86a376a4c7d98dad9b6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py Log Message: ----------- Do not remove tools from other installed revisions when uninstalling TS repo Multiple installed revisions of a repository can provide the same version of a tool, e.g. for the repository https://toolshed.g2.bx.psu.edu/view/nilesh/rseqc only one tool out of 22 has a different version in revision 57 with respect to revision 56. In this case, when uninstalling one repository, the tools with the same guid were removed also from the other repository revisions in the `shed_tool_conf` file. This can be prevented by checking also the tool path. Commit: f84a29b9545d544d8d1bbe0a433f3e8dd647cbaf https://github.com/galaxyproject/galaxy/commit/f84a29b9545d544d8d1bbe0a433f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M templates/webapps/tool_shed/common/common.mako M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #7300 from nsoranzo/toolshed_fixes Do not remove tools from other installed revisions when uninstalling TS repo Compare: https://github.com/galaxyproject/galaxy/compare/71b01b1be3f7...f84a29b9545d

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[galaxyproject/usegalaxy-playbook] cce48a: usegalaxy.* integration updates for Test
by Nate Coraor 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cce48a7764ed202c79dd9e0407a7e7eeb2d3c3c1 https://github.com/galaxyproject/usegalaxy-playbook/commit/cce48a7764ed202c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/test/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/migrated_tools_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- usegalaxy.* integration updates for Test

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[galaxyproject/usegalaxy-playbook] eacbc7: Test tool_conf.xml changes for usegalaxy.* integra...
by Nate Coraor 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: eacbc7190e92f0055b11c856eda6a0b6c9c402b9 https://github.com/galaxyproject/usegalaxy-playbook/commit/eacbc7190e92f005… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/test/files/galaxy/config/tool_conf.xml Log Message: ----------- Test tool_conf.xml changes for usegalaxy.* integration Commit: e233c920e97a6b756db9951bf058d6ac4ee39bcd https://github.com/galaxyproject/usegalaxy-playbook/commit/e233c920e97a6b75… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/migrated_tools_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Partial Test mutable config fixes for usegalaxy.* integration Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/4aeeb45287d2...…

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[galaxyproject/galaxy] 428c66: Remove errant space in intermine_simple_display.lo...
by Martin Cech 04 Feb '19

04 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 428c6632f0196ebd45a42d1c61776ac3402e985f https://github.com/galaxyproject/galaxy/commit/428c6632f0196ebd45a42d1c6177… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M tool-data/intermine_simple_display.loc.sample Log Message: ----------- Remove errant space in intermine_simple_display.loc.sample Commit: 526bebbb2817376b4c4e131890d75d1ea76b0e85 https://github.com/galaxyproject/galaxy/commit/526bebbb2817376b4c4e131890d7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M tool-data/intermine_simple_display.loc.sample Log Message: ----------- Merge pull request #7298 from blankenberg/intermine-loc-fix-19.01 [19.01] Remove errant space in intermine_simple_display.loc.sample Compare: https://github.com/galaxyproject/galaxy/compare/49cbad5debb6...526bebbb2817

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[galaxyproject/galaxy] 7dd921: Add longer pauses for some selenium tests, mark as...
by Aysam Guerler 04 Feb '19

04 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7dd9213fd874a4bf12d0eee86f03c48dd467a6f2 https://github.com/galaxyproject/galaxy/commit/7dd9213fd874a4bf12d0eee86f03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_custom_builds.py Log Message: ----------- Add longer pauses for some selenium tests, mark as slow renders for easier tracking down and fixing. Commit: d59352224c8f41ba8a1a9219b2bafa24e1a1f142 https://github.com/galaxyproject/galaxy/commit/d59352224c8f41ba8a1a9219b2ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/driver_factory.py Log Message: ----------- Set chrome to run headlessly -- todo configure via env var or switch Commit: 78c66f260c4bad5b2d632919fe14307602c8fb4e https://github.com/galaxyproject/galaxy/commit/78c66f260c4bad5b2d632919fe14… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Wait for logout redirect. Commit: 9e879b731f27d7b17161c83a60ef559aa529ec63 https://github.com/galaxyproject/galaxy/commit/9e879b731f27d7b17161c83a60ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_custom_builds.py Log Message: ----------- Drop now unused slowrender Commit: 817a8469b69e37c48e72a081a75d5c734e636624 https://github.com/galaxyproject/galaxy/commit/817a8469b69e37c48e72a081a75d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M test/galaxy_selenium/cli.py M test/galaxy_selenium/driver_factory.py M test/selenium_tests/framework.py Log Message: ----------- Tie chrome native headless mode into existing HEADLESS logic, functioning with or without pyvirtualdisplay. Commit: 71b01b1be3f70f239fe9114b43eeef87fd9801d9 https://github.com/galaxyproject/galaxy/commit/71b01b1be3f70f239fe9114b43ee… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M test/galaxy_selenium/cli.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #7287 from dannon/slow_selenium_tests Fix remaining selenium tests and add headless testing option. Compare: https://github.com/galaxyproject/galaxy/compare/645031578d31...71b01b1be3f7

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[galaxyproject/usegalaxy-playbook] 4aeeb4: update TTS
by Martin Cech 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4aeeb45287d27fc2e4cf19ccfae7e2d31ecc8e77 https://github.com/galaxyproject/usegalaxy-playbook/commit/4aeeb45287d27fc2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update TTS

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[galaxyproject/usegalaxy-playbook] 6f0e88: update MTS
by Martin Cech 04 Feb '19

04 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f0e88a96ebb95fceecc50ba7e93fd4ad02bc0fe https://github.com/galaxyproject/usegalaxy-playbook/commit/6f0e88a96ebb95fc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update MTS

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[galaxyproject/galaxy] 8293b5: fix ObjectNotFound exception when exporting an his...
by John Chilton 04 Feb '19

04 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8293b5bb0a3f93a37907beb47489646d22aaad07 https://github.com/galaxyproject/galaxy/commit/8293b5bb0a3f93a37907beb47489… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- fix ObjectNotFound exception when exporting an history Commit: 645031578d31801eee84ac79013d2da358212078 https://github.com/galaxyproject/galaxy/commit/645031578d31801eee84ac79013d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #7286 from abretaud/export_bug Fix ObjectNotFound exception when exporting an history Compare: https://github.com/galaxyproject/galaxy/compare/e8e3b0ca15b4...645031578d31

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[galaxyproject/galaxy] 6589bf: Drop support for Python 3.4. Officially support Py...
by Marius van den Beek 03 Feb '19

03 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6589bf3314faf7425bdd8b680a6e47a21fba0163 https://github.com/galaxyproject/galaxy/commit/6589bf3314faf7425bdd8b680a6e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: M .travis.yml M scripts/check_python.py M tox.ini Log Message: ----------- Drop support for Python 3.4. Officially support Python >=3.5 xref. https://github.com/galaxyproject/galaxy/issues/7260 Commit: 82adf46a8a8c50458f7cf3dde35c6b24ab1ed2bc https://github.com/galaxyproject/galaxy/commit/82adf46a8a8c50458f7cf3dde35c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Speficy sniff order for BAM datatypes Fix flakey ``test_upload_datatype_auto`` integration test: https://jenkins.galaxyproject.org/job/docker-integration-py3/125/testReport… Commit: e8e3b0ca15b41fa4c573323e5c17ac51ad411eda https://github.com/galaxyproject/galaxy/commit/e8e3b0ca15b41fa4c573323e5c17… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-03 (Sun, 03 Feb 2019) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M scripts/check_python.py M tox.ini Log Message: ----------- Merge pull request #7291 from nsoranzo/drop_python3.4 Drop support for Python 3.4. Officially support Python >=3.5 Compare: https://github.com/galaxyproject/galaxy/compare/8c2066f07ac7...e8e3b0ca15b4

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[galaxyproject/galaxy] 37a9f2: Update logging config docs:
by Daniel Blankenberg 02 Feb '19

02 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 37a9f2bcea99ea55f7b36b94aa481558702ca897 https://github.com/galaxyproject/galaxy/commit/37a9f2bcea99ea55f7b36b94aa48… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-07 (Mon, 07 Jan 2019) Changed paths: M doc/Makefile M doc/source/admin/config_logging.rst Log Message: ----------- Update logging config docs: - The example for split file logging was invalid (referenced the nonexistent "generic" formatter) - Switch YAML dicts from 4- to 2-space indent to match the indentation style in galaxy.yml.sample - Document setting the message format with the YAML config - Reword a few things to hopefully be a bit clearer Commit: 79672df45221e4417d2c363bb262c19a2eb48b1f https://github.com/galaxyproject/galaxy/commit/79672df45221e4417d2c363bb262… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M config/job_conf.xml.sample_advanced M doc/source/admin/scaling.md Log Message: ----------- Update documentation for handler assignment method configurability and remove some legacy stuff. Commit: e9773f17335bea2d9106aa364d29f1f53454c883 https://github.com/galaxyproject/galaxy/commit/e9773f17335bea2d9106aa364d29… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M doc/source/admin/config_logging.rst Log Message: ----------- Minor spello Commit: 35c60489e8d52a47e82ae4462dfd7af5ced26f2b https://github.com/galaxyproject/galaxy/commit/35c60489e8d52a47e82ae4462dfd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-09 (Wed, 09 Jan 2019) Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md Log Message: ----------- Fixed link to proxy_package_layout in proxy docs Commit: 9a133e91f84d31e0c4e39c36301a368d66c48508 https://github.com/galaxyproject/galaxy/commit/9a133e91f84d31e0c4e39c36301a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Remove spurious characters Co-Authored-By: natefoo <nate(a)bx.psu.edu> Commit: 74fcf12fa0968ef448fecb3f0ff9bd4736f91cd2 https://github.com/galaxyproject/galaxy/commit/74fcf12fa0968ef448fecb3f0ff9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Incorporate suggestions from @nsoranzo Commit: 49cbad5debb649013e142134b3b4ad8361125914 https://github.com/galaxyproject/galaxy/commit/49cbad5debb649013e142134b3b4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2019-02-02 (Sat, 02 Feb 2019) Changed paths: M config/job_conf.xml.sample_advanced M doc/Makefile M doc/source/admin/apache.md M doc/source/admin/config_logging.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #7191 from natefoo/admin-docs-19.01 [19.01] Properly document handler assignment method configuration and fix logging configuration docs Compare: https://github.com/galaxyproject/galaxy/compare/038d1a1d83fa...49cbad5debb6

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galaxy-commits February 2019