February 2019 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 9258b2: Define doctype method on XMLParser target
by Nicola Soranzo 06 Feb '19

06 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9258b28e7d2c5cdec497f723b7b124619546d52b https://github.com/galaxyproject/galaxy/commit/9258b28e7d2c5cdec497f723b7b1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Define doctype method on XMLParser target That should silence some Deprecation Warnings. Commit: 28240d83536abac75288f4fb79b981a6cc6a83f1 https://github.com/galaxyproject/galaxy/commit/28240d83536abac75288f4fb79b9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Remove deprecated U mode option Commit: 6c8a523d59c9783ed6d444a5dad8340837cc1ebe https://github.com/galaxyproject/galaxy/commit/6c8a523d59c9783ed6d444a5dad8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/__init__.py M lib/galaxy/util/compression_utils.py Log Message: ----------- Replace more instances of 'U' mode Commit: 2ec2933e0ebbe4e33a27e8d855f9f0fc771c6ff5 https://github.com/galaxyproject/galaxy/commit/2ec2933e0ebbe4e33a27e8d855f9… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/util/compression_utils.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #7303 from mvdbeek/xml_parser_deprecation_warning Define doctype method on XMLParser target Compare: https://github.com/galaxyproject/galaxy/compare/3b49be59a12c...2ec2933e0ebb

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[galaxyproject/usegalaxy-playbook] 9aad46: Combine BCF Tools in to VCF Manipulation
by Nate Coraor 05 Feb '19

05 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9aad46a8b71363490f403fc10380586af2500eb7 https://github.com/galaxyproject/usegalaxy-playbook/commit/9aad46a8b7136349… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Combine BCF Tools in to VCF Manipulation

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[galaxyproject/usegalaxy-playbook] 612d51: Use CVMFS path in Test shed_tool_conf.xml
by Nate Coraor 05 Feb '19

05 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 612d5183bfd439084157666bd277faede17dbfe9 https://github.com/galaxyproject/usegalaxy-playbook/commit/612d5183bfd43908… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Use CVMFS path in Test shed_tool_conf.xml Commit: 7ef7bbc7d3e5e8475eb8737a2187d460fe0d959b https://github.com/galaxyproject/usegalaxy-playbook/commit/7ef7bbc7d3e5e847… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/main/files/galaxy/var/migrated_tools_conf.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Point Main migrated_tools_conf.xml and shed_tool_conf.xml at actual CVMFS paths instead of symlinks to CVMFS. Commit: bd4b0ddfb0293fcf3bee3b7636680ec0d4e34a79 https://github.com/galaxyproject/usegalaxy-playbook/commit/bd4b0ddfb0293fcf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/17c556e0caec...…

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[galaxyproject/usegalaxy-playbook] 17c556: update Test
by Martin Cech 05 Feb '19

05 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 17c556e0caec30b6994cd035070e0b3bf7f7ce2d https://github.com/galaxyproject/usegalaxy-playbook/commit/17c556e0caec30b6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update Test

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[galaxyproject/galaxy] 4df1de: Map over multiple=true in workflow run
by Martin Cech 05 Feb '19

05 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4df1de38ba390ee6513bc85fbb0643e6e152bd25 https://github.com/galaxyproject/galaxy/commit/4df1de38ba390ee6513bc85fbb06… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Map over multiple=true in workflow run There is some unfortunate divergence between the mapping over code in tool runs vs workflow runs. Without this patch a list:list input to a multiple="true" data input would get fully reduced in workflow, while tool runs would just reduce the inner collection (and I think that's the correct behavior). Commit: cf68cbe907729283a8a359d9a8dbcb0013ebcee5 https://github.com/galaxyproject/galaxy/commit/cf68cbe907729283a8a359d9a8db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Verify that list:list will be reduced to list in multi data input Commit: a36b56e6940cf8e406ebca90114e2a9974e50e0d https://github.com/galaxyproject/galaxy/commit/a36b56e6940cf8e406ebca90114e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Drop redundant wait for history wait_for_invocation_and_jobs does that already, thx @nsoranzo. Commit: c4fbe94bcfeef2acc5edf516a625578c7578feff https://github.com/galaxyproject/galaxy/commit/c4fbe94bcfeef2acc5edf516a625… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #7302 from mvdbeek/dont_reduce_list_list_in_multi_data_input_workflow_step [19.01] Don't reduce list:list in multi data input workflow step Commit: 3b49be59a12cf886040e894d3b1b1e644ff7cfa4 https://github.com/galaxyproject/galaxy/commit/3b49be59a12cf886040e894d3b1b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e4d798cecdcb...3b49be59a12c

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[galaxyproject/galaxy] 9aed42: Determine collection_type for all workflow steps
by Dannon 05 Feb '19

05 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9aed429a359d0fdf3933417aae89e81e6981c8f2 https://github.com/galaxyproject/galaxy/commit/9aed429a359d0fdf3933417aae89… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Determine collection_type for all workflow steps Commit: 6a4307609d90264b45104ae017e1056d055e7170 https://github.com/galaxyproject/galaxy/commit/6a4307609d90264b45104ae017e1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Unit test resolve_collection_type Commit: 65583ba4034302e02c87bf2db8c84fb7b83c0dee https://github.com/galaxyproject/galaxy/commit/65583ba4034302e02c87bf2db8c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Don't fail if tool is not installed Commit: ef50e872973710774cf62fc5eb3b7a761e503259 https://github.com/galaxyproject/galaxy/commit/ef50e872973710774cf62fc5eb3b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Only fill collection_type for subworkflows, the top level stuff is managed by the client Commit: 5ac0802dd71236801ed0709f9b6df4014a60f850 https://github.com/galaxyproject/galaxy/commit/5ac0802dd71236801ed0709f9b6d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Don't display subworkflow inputs as workflow_outputs Commit: c5726c33b27756c1b5768f654b59935265160341 https://github.com/galaxyproject/galaxy/commit/c5726c33b27756c1b5768f654b59… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/workflow/modules.py Log Message: ----------- Add input collection_type when including subworkflow Commit: 667f8aa761df88d48f1c00dd7fd98bb764e0032d https://github.com/galaxyproject/galaxy/commit/667f8aa761df88d48f1c00dd7fd9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-28 (Mon, 28 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py M test/unit/workflows/workflow_support.py Log Message: ----------- Only add collection_type if collection_type has been specified We don't force the collection_type to be set in any way. We might want to think about defaulting to list if not specified, but that's not for now. Commit: e4d798cecdcb819c2f5ef4ee6caf8aa64b53faba https://github.com/galaxyproject/galaxy/commit/e4d798cecdcb819c2f5ef4ee6caf… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #7254 from mvdbeek/subworkflow_connectivity Determine collection_type for all workflow steps Compare: https://github.com/galaxyproject/galaxy/compare/0fba7f30c13c...e4d798cecdcb

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[galaxyproject/usegalaxy-playbook] a08bd2: Tool panel fixes for Assembly/Annotation/Mapping
by Nate Coraor 05 Feb '19

05 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a08bd26ccd758142c11070c90cab0dc42b512c32 https://github.com/galaxyproject/usegalaxy-playbook/commit/a08bd26ccd758142… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 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: ----------- Tool panel fixes for Assembly/Annotation/Mapping Commit: 991d4f38a48e34e5ce4299cef2beb554b29cc32f https://github.com/galaxyproject/usegalaxy-playbook/commit/991d4f38a48e34e5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 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: ----------- Test usegalaxy.* toolbox sync Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/cce48a7764ed...…

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[galaxyproject/galaxy] 4df1de: Map over multiple=true in workflow run
by Nicola Soranzo 05 Feb '19

05 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 4df1de38ba390ee6513bc85fbb0643e6e152bd25 https://github.com/galaxyproject/galaxy/commit/4df1de38ba390ee6513bc85fbb06… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Map over multiple=true in workflow run There is some unfortunate divergence between the mapping over code in tool runs vs workflow runs. Without this patch a list:list input to a multiple="true" data input would get fully reduced in workflow, while tool runs would just reduce the inner collection (and I think that's the correct behavior). Commit: cf68cbe907729283a8a359d9a8dbcb0013ebcee5 https://github.com/galaxyproject/galaxy/commit/cf68cbe907729283a8a359d9a8db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Verify that list:list will be reduced to list in multi data input Commit: a36b56e6940cf8e406ebca90114e2a9974e50e0d https://github.com/galaxyproject/galaxy/commit/a36b56e6940cf8e406ebca90114e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/api/test_workflows.py Log Message: ----------- Drop redundant wait for history wait_for_invocation_and_jobs does that already, thx @nsoranzo. Commit: c4fbe94bcfeef2acc5edf516a625578c7578feff https://github.com/galaxyproject/galaxy/commit/c4fbe94bcfeef2acc5edf516a625… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #7302 from mvdbeek/dont_reduce_list_list_in_multi_data_input_workflow_step [19.01] Don't reduce list:list in multi data input workflow step Compare: https://github.com/galaxyproject/galaxy/compare/526bebbb2817...c4fbe94bcfee

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[galaxyproject/galaxy] 45a962: Update proxy dependencies -- mine wouldn't build a...
by Martin Cech 05 Feb '19

05 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45a962a8a8930ad6706372e4d770a23cd1ee777c https://github.com/galaxyproject/galaxy/commit/45a962a8a8930ad6706372e4d770… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-11 (Fri, 11 Jan 2019) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Update proxy dependencies -- mine wouldn't build anymore with an older version of sqlite3. I'm hoping the versions I've updated to are backwards compatible in terms of compilation (seem to be in terms of functionality -- it's working for me), but I'd appreciate someone else checking. Commit: 0fba7f30c13c38f28ada0eb90fc1fd7816704a4d https://github.com/galaxyproject/galaxy/commit/0fba7f30c13c38f28ada0eb90fc1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge pull request #7208 from dannon/update_ie_proxy Update IE proxy dependencies Compare: https://github.com/galaxyproject/galaxy/compare/03463f4b0598...0fba7f30c13c

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[galaxyproject/galaxy] 37a9f2: Update logging config docs:
by Nicola Soranzo 05 Feb '19

05 Feb '19

Branch: refs/heads/dev 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: bdc6243a78b0fcf1e0d0a89670ec19dcb3aa9479 https://github.com/galaxyproject/galaxy/commit/bdc6243a78b0fcf1e0d0a89670ec… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Darker tool form in workflow editor Commit: 038d1a1d83fac689e0d00f85cb59057bfe79bfcc https://github.com/galaxyproject/galaxy/commit/038d1a1d83fac689e0d00f85cb59… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Revert "Darker tool form in workflow editor" This reverts commit bdc6243a78b0fcf1e0d0a89670ec19dcb3aa9479. 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 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 Commit: 03463f4b0598df5619def5230de3fb758b4090ba https://github.com/galaxyproject/galaxy/commit/03463f4b0598df5619def5230de3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-05 (Tue, 05 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 M tool-data/intermine_simple_display.loc.sample Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f84a29b9545d...03463f4b0598

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