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

[galaxyproject/galaxy] 0c8dad: Seemingly fix #2806.
by GitHub 08 Sep '16

08 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c8dadcede0609ed1a8aed997c57adceaf8dce83 https://github.com/galaxyproject/galaxy/commit/0c8dadcede0609ed1a8aed997c57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-06 (Tue, 06 Sep 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Seemingly fix #2806. I guess this would make sense if somehow the step of this workflow has its tool parameters double wrapped. Commit: d98dcd75db307de955391c46e4121a0cd3036f3e https://github.com/galaxyproject/galaxy/commit/d98dcd75db307de955391c46e412… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #2898 from jmchilton/fix_2806 Seemingly fix #2806. Compare: https://github.com/galaxyproject/galaxy/compare/2d36ab52dee7...d98dcd75db30

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[galaxyproject/galaxy] b710ed: Fix over encoding of dataset ids
by GitHub 07 Sep '16

07 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b710ed1e8519fc6ed85f1d9cef4b63e679294a93 https://github.com/galaxyproject/galaxy/commit/b710ed1e8519fc6ed85f1d9cef4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-06 (Tue, 06 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix over encoding of dataset ids Commit: 94338632e005da8a9e90eabdbf915b9102b9308e https://github.com/galaxyproject/galaxy/commit/94338632e005da8a9e90eabdbf91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Rename lda id parameter Commit: 259e6730c21dae72c6bd60ba38b52f6954b9ca83 https://github.com/galaxyproject/galaxy/commit/259e6730c21dae72c6bd60ba38b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Rename to use_security Commit: 2d36ab52dee7085628f30ecd58c7c920158804d8 https://github.com/galaxyproject/galaxy/commit/2d36ab52dee7085628f30ecd58c7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2902 from guerler/fix_id_storage Fix over encoding of dataset ids Compare: https://github.com/galaxyproject/galaxy/compare/69ee5afaeca5...2d36ab52dee7

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[galaxyproject/galaxy] d6b934: Extend import order linting to all of galaxy-lib w...
by GitHub 07 Sep '16

07 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6b9348f377d48f85286fdf57b826ec99e29a856 https://github.com/galaxyproject/galaxy/commit/d6b9348f377d48f85286fdf57b82… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/lazy_process.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/permutations.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/sockets.py M lib/galaxy/util/sqlite.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M setup.cfg M test/unit/test_objectstore.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py Log Message: ----------- Extend import order linting to all of galaxy-lib w/fixes. Includes a bit linting of order for galaxy.util. Commit: 825c7287a57dabe465f86bb5b66730aba080d000 https://github.com/galaxyproject/galaxy/commit/825c7287a57dabe465f86bb5b667… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M lib/galaxy/tools/parser/yaml.py M lib/galaxy/util/topsort.py Log Message: ----------- Lint fixes thanks to @nsoranzo's eagle eyes. Commit: 69ee5afaeca5dce6acb814cf292a009e9fd2f0c5 https://github.com/galaxyproject/galaxy/commit/69ee5afaeca5dce6acb814cf292a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/tags.py M lib/galaxy/tools/verify/asserts/xml.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/lazy_process.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/permutations.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/sockets.py M lib/galaxy/util/sqlite.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M setup.cfg M test/unit/test_objectstore.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py Log Message: ----------- Merge pull request #2889 from jmchilton/import-order-linting Extend import order linting to all of galaxy-lib w/fixes. Compare: https://github.com/galaxyproject/galaxy/compare/cbd55b20d373...69ee5afaeca5

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[galaxyproject/galaxy] 4f3c44: Move the registration of the start function into t...
by GitHub 07 Sep '16

07 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 4f3c44f3ad386a667f156f39d1af44bf23b7a8ab https://github.com/galaxyproject/galaxy/commit/4f3c44f3ad386a667f156f39d1af… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Move the registration of the start function into the ToolConfWatcher itself so it doesn't have to be called by things that instantiate it. Fixes #2831. Commit: 6631367b7cd4f2049426f3554eef6da626b83837 https://github.com/galaxyproject/galaxy/commit/6631367b7cd4f2049426f3554eef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Unused import, cleanup for #2856 Commit: 3e65a165b722740b48ece5dab36a2a28cfa7681c https://github.com/galaxyproject/galaxy/commit/3e65a165b722740b48ece5dab36a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- fix inclusion of release notes in announcement Commit: c98331eddd3f8a57cedca313249798e1e45a9555 https://github.com/galaxyproject/galaxy/commit/c98331eddd3f8a57cedca3132497… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #2856 from natefoo/postfork-tool-conf-watcher-test-fix [16.07] Postfork tool conf watcher test fix Commit: 53a5b76ff2e47bbf821845e0d2170240902a70eb https://github.com/galaxyproject/galaxy/commit/53a5b76ff2e47bbf821845e0d217… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #2860 from dannon/postfork-tool-conf-watcher-test-fix [16.07] Unused import cleanup for #2856 Commit: e891c5755f59e8865cbee56cd4fcc8e5f4bbd0af https://github.com/galaxyproject/galaxy/commit/e891c5755f59e8865cbee56cd4fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Merge pull request #2859 from martenson/fix-notes-include [16.07] fix inclusion of release notes in the announcement Commit: d1821fed475a4261c007de3627cb3eeb42d53a1f https://github.com/galaxyproject/galaxy/commit/d1821fed475a4261c007de3627cb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- disable conda_auto_init Commit: 52768c0c42313c08f25ba07b47ccf2bed28248f4 https://github.com/galaxyproject/galaxy/commit/52768c0c42313c08f25ba07b47cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #2863 from martenson/release_16.07 [16.07] backport disable conda_auto_init Commit: 6724146e7d09e5c0ac4f19d96e600d14831a8abe https://github.com/galaxyproject/galaxy/commit/6724146e7d09e5c0ac4f19d96e60… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix three conda bugs. - Don't attempt file lock if don't have write access for lock. - Set disabled to False if conda present and auto_init is False. - Use the correct parent path for conda_prefix (if default parent path is overridden). Commit: c01ce21e2cdb7b229dd8ced14e4e2c1c7fdf294c https://github.com/galaxyproject/galaxy/commit/c01ce21e2cdb7b229dd8ced14e4e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2864 from jmchilton/conda_fixes [16.07] Fix three conda bugs. Commit: e320b1aaa70aea38b7108ca6ae372b1d06fd30bc https://github.com/galaxyproject/galaxy/commit/e320b1aaa70aea38b7108ca6ae37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-07 (Wed, 07 Sep 2016) Changed paths: M config/galaxy.ini.sample M doc/source/releases/16.07.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge branch 'release_16.07' Compare: https://github.com/galaxyproject/galaxy/compare/ddc9c647b2d2...e320b1aaa70a

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[galaxyproject/usegalaxy-playbook] 7003a6: Only run the static playbook on webservers
by GitHub 06 Sep '16

06 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7003a635d71861b894b344d3857681c3e591288d https://github.com/galaxyproject/usegalaxy-playbook/commit/7003a635d71861b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-06 (Tue, 06 Sep 2016) Changed paths: M galaxy_static.yml Log Message: ----------- Only run the static playbook on webservers

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[galaxyproject/usegalaxy-playbook] 9b0dc4: Updated landing page slides. Dropped CPT; added GA...
by GitHub 06 Sep '16

06 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9b0dc4c42f091e3cb7a1bbb3b47397658b3628ba https://github.com/galaxyproject/usegalaxy-playbook/commit/9b0dc4c42f091e3c… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-09-06 (Tue, 06 Sep 2016) Changed paths: A files/galaxy/common/static/welcome_img/GAT2016EarlyReg.png A files/galaxy/common/static/welcome_img/SG2016.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated landing page slides. Dropped CPT; added GAT2016 Early Reg and SG2016 slides.

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[galaxyproject/galaxy] d092bd: Enable new run workflow form by default
by GitHub 06 Sep '16

06 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d092bd8ec2d29bd05a701c0edae1c915e392d257 https://github.com/galaxyproject/galaxy/commit/d092bd8ec2d29bd05a701c0edae1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Enable new run workflow form by default Commit: e510f86a05b2a8ad368e0b99f521bfcce207cfc1 https://github.com/galaxyproject/galaxy/commit/e510f86a05b2a8ad368e0b99f521… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Update default value in sample config file Commit: cbd55b20d373538d2b8019344dd08a0fd190752c https://github.com/galaxyproject/galaxy/commit/cbd55b20d373538d2b8019344dd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-09-06 (Tue, 06 Sep 2016) Changed paths: M config/galaxy.ini.sample M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2895 from guerler/activate_new_run_form Enable new run workflow form Compare: https://github.com/galaxyproject/galaxy/compare/61fb26181c7d...cbd55b20d373

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[galaxyproject/galaxy] 569ceb: Try reloading tool via control_task
by GitHub 02 Sep '16

02 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 569ceb4405bef72c420c91c86f4c203f6d7ed29f https://github.com/galaxyproject/galaxy/commit/569ceb4405bef72c420c91c86f4c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Try reloading tool via control_task Commit: 1223c420cb48ef05db61303ef784ff276716cdc3 https://github.com/galaxyproject/galaxy/commit/1223c420cb48ef05db61303ef784… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Explicitly monitor shed_tool_conf for changes Commit: 1d04755fa39657bb824ca986e41224e77d59d35f https://github.com/galaxyproject/galaxy/commit/1d04755fa39657bb824ca986e412… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Reference app instead of self when reloading toolbox Commit: 6e4897dee7d66587d75b445f9211b51f07490241 https://github.com/galaxyproject/galaxy/commit/6e4897dee7d66587d75b445f9211… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Do not load individual new toolpanel elements (We rely on the tool watcher to reload the toolbox) Commit: f7693802ce0d2e555cb283a09d0a83740e8664e2 https://github.com/galaxyproject/galaxy/commit/f7693802ce0d2e555cb283a09d0a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Remove in-memory removal of tools (rely on toolbox reload) Commit: 7b259fb10a5f1289ba81ec749a1e86ccf3fb7303 https://github.com/galaxyproject/galaxy/commit/7b259fb10a5f1289ba81ec749a1e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove one more unused panel manipulation function Commit: 128ee9b72a6c7f693a990c65b1c4b34d9be193c5 https://github.com/galaxyproject/galaxy/commit/128ee9b72a6c7f693a990c65b1c4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Remove unused variable Commit: 81bf7b382bc1003c0d1a3b0a019ea7e57d6ecce9 https://github.com/galaxyproject/galaxy/commit/81bf7b382bc1003c0d1a3b0a019e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M test/unit/tools/test_watcher.py Log Message: ----------- Start conf_watcher thread in unit tests Commit: e340fd4e06f7b8a2063448bad8e2c594af39cdb9 https://github.com/galaxyproject/galaxy/commit/e340fd4e06f7b8a2063448bad8e2… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M test/unit/tools/test_watcher.py Log Message: ----------- Wait before triggering a callback in test_watcher.py Commit: 3206421b91a305d1e38672a1bccd52c732705266 https://github.com/galaxyproject/galaxy/commit/3206421b91a305d1e38672a1bccd… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Remove update_shed_conf test We do not update the toolbox in memory, so this test is obsolete Commit: fe158de11109140b22c408cd6640b547ffd4db30 https://github.com/galaxyproject/galaxy/commit/fe158de11109140b22c408cd6640… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) 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: ----------- Remove panel_manager tests for deactivated tools Deactivate tests that rely on deactivating, but not removing entries from tool_conf. For tests that test changes in tool_panel, load a new toolbox after making the changes. Commit: ad86e2c7840fa9129263fdfb144959c158653874 https://github.com/galaxyproject/galaxy/commit/ad86e2c7840fa9129263fdfb1449… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py Log Message: ----------- Add sleep to allow toolbox to finish loading Commit: ded1db8b3834bf3de6897b2163a9d208828d259d https://github.com/galaxyproject/galaxy/commit/ded1db8b3834bf3de6897b2163a9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py Log Message: ----------- Remove test for deactivated tools and sections These are tests that verify that deactivated tools were present in the correct tool panel section. Commit: 693eb5d0c91061fdbe052b41be1e78f4c58f57cb https://github.com/galaxyproject/galaxy/commit/693eb5d0c91061fdbe052b41be1e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py Log Message: ----------- Wait 2 seconds after touch shed_tool_conf.xml The file watcher monitors for changes every second, so 2 seconds should be enough to let tests that check the tool panel after installing new tools pass. Commit: 2fb4045abd61b9ccb1afb4e5e422ad6e73167db8 https://github.com/galaxyproject/galaxy/commit/2fb4045abd61b9ccb1afb4e5e422… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Also reload data managers upon touching data_manager.conf Commit: f6fc5ed44299f2d1a9ac1c966d43281fd9515bf0 https://github.com/galaxyproject/galaxy/commit/f6fc5ed44299f2d1a9ac1c966d43… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Shut down old data manager watchers Commit: abd4fa611a3f1d4d089a03aef48ecb43383bb101 https://github.com/galaxyproject/galaxy/commit/abd4fa611a3f1d4d089a03aef48e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py Log Message: ----------- Implement hashing for tool conf watcher If modification time of watched files changes, only trigger event if hashes differ as well Commit: 49ab74827cd0905cd0fa62eee7a5643b43ad41d9 https://github.com/galaxyproject/galaxy/commit/49ab74827cd0905cd0fa62eee7a5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Log who's triggering a reload Commit: a2669c565ae7c25bcd20c9831a470bbc0731597c https://github.com/galaxyproject/galaxy/commit/a2669c565ae7c25bcd20c9831a47… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Add back integrated_tool_panel saving Commit: 6fc46a8c46549bc43fca00cfbd2e32b07db158d5 https://github.com/galaxyproject/galaxy/commit/6fc46a8c46549bc43fca00cfbd2e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Directly reload toolbox or data manager when watcher triggers reload Commit: 054fbd05cb2ca3918f0dd2819cc71e5485ef4580 https://github.com/galaxyproject/galaxy/commit/054fbd05cb2ca3918f0dd2819cc7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Use the tool_data_tables.tool_data_path, to avoid persisting the temporary in-memory path to the data table Commit: 612eea85e6e2322d277f4210005d2efbddaae3e1 https://github.com/galaxyproject/galaxy/commit/612eea85e6e2322d277f4210005d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Fix reload thread for uwsgi workers. and fix typos Commit: 1bc84e0b4f5a77d018126656fc2808ed66c4712e https://github.com/galaxyproject/galaxy/commit/1bc84e0b4f5a77d018126656fc28… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Do not call start() method of watchter as this happens when it starts watching a file. Commit: b8695b36280f195242215c56cffad9aff5a7fad4 https://github.com/galaxyproject/galaxy/commit/b8695b36280f195242215c56cffa… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- One last attempt to revive launched thread Commit: 9e36a15e22f92fd3913a1dbed0700bcae91b61e7 https://github.com/galaxyproject/galaxy/commit/9e36a15e22f92fd3913a1dbed070… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Transplant tool conf watcher thread Commit: 95c0e3cbf78e45f7786cab918835004dc67c156d https://github.com/galaxyproject/galaxy/commit/95c0e3cbf78e45f7786cab918835… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Also reload conf_watchers for data managers Commit: c0cef19eb7a68e61ac30d9eb55b6bef14705648d https://github.com/galaxyproject/galaxy/commit/c0cef19eb7a68e61ac30d9eb55b6… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Reload data managers after reloading the toolbox Commit: 3d42be5f234d837ff5fa3792c53d138d3e28fcac https://github.com/galaxyproject/galaxy/commit/3d42be5f234d837ff5fa3792c53d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Trigger event with lock Commit: 271959d1345077baa064c60fe79ff00a6ed0b021 https://github.com/galaxyproject/galaxy/commit/271959d1345077baa064c60fe79f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/tool_shed/metadata/metadata_generator.py M test/unit/tools/test_watcher.py Log Message: ----------- Reload data table managers and data tables ... before reloading data managers. Data managers need to have access to the data tables, so that they can process the results. Do not explicitly start watcher thread for shed_data_manager_conf changes. Commit: f92d496bd9ae42387e5017e2ef84a032de6e49ea https://github.com/galaxyproject/galaxy/commit/f92d496bd9ae42387e5017e2ef84… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove debugging statements and mention uwsgi/threads in line Commit: 7afb25d5fbf8bcb37d4c9fc7e25b20b8d8373011 https://github.com/galaxyproject/galaxy/commit/7afb25d5fbf8bcb37d4c9fc7e25b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Wait for shed_data_manager_conf watcher to pick up changes Commit: a19f67f8be85c4d5b459082ea9343cbda0a298b3 https://github.com/galaxyproject/galaxy/commit/a19f67f8be85c4d5b459082ea934… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Try locking load_item Commit: 426ea3b726a085f1a89033ed875584468db7b321 https://github.com/galaxyproject/galaxy/commit/426ea3b726a085f1a89033ed8755… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Keep a count of reloads Commit: c4aa171ae4bc16667b082122ef14dfc0f08891c8 https://github.com/galaxyproject/galaxy/commit/c4aa171ae4bc16667b082122ef14… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Always wait for reload action to be finished Commit: 7f893f39f6d1087afe50af9d9a61da77fcbe14db https://github.com/galaxyproject/galaxy/commit/7f893f39f6d1087afe50af9d9a61… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py M test/unit/tools_support.py Log Message: ----------- Mock the Lock; fix linting problems Commit: c1d66d1fbc7281cb2cd5b050e8516818093d3e6a https://github.com/galaxyproject/galaxy/commit/c1d66d1fbc7281cb2cd5b050e851… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M test/unit/tools_support.py Log Message: ----------- One more linting fix Commit: 4adc872e5864d9a8262948a56a4552fbafe68390 https://github.com/galaxyproject/galaxy/commit/4adc872e5864d9a8262948a56a45… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M test/unit/tools_support.py Log Message: ----------- Fix indentation Commit: 99acb36da32ec2d2d4d7d1ce7cdc4da426e51645 https://github.com/galaxyproject/galaxy/commit/99acb36da32ec2d2d4d7d1ce7cdc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M test/unit/tools_support.py Log Message: ----------- Add server_name to unit test app's config. Required for messaging stuff. Commit: 9f7c749638340fb63ac00a417a9e328875296885 https://github.com/galaxyproject/galaxy/commit/9f7c749638340fb63ac00a417a9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/unit/tools_support.py Log Message: ----------- Fix test case for tool manager. Commit: 9a9a1f9becf185db5a778f1436913bc6942b2ac3 https://github.com/galaxyproject/galaxy/commit/9a9a1f9becf185db5a778f143691… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Lint for last commit. Commit: 4479bcebbe6984c06d0b5b9411d6d9e8bc2f22ca https://github.com/galaxyproject/galaxy/commit/4479bcebbe6984c06d0b5b9411d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M doc/source/admin/conda_faq.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py R lib/galaxy/tools/toolbox/requirements.py A lib/galaxy/util/filelock.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py R lib/galaxy/web/proxy/filelock.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into reload_toolbox_across_handlers Commit: 53d387d771b3bb95cd17cf0c74ec90099122f376 https://github.com/galaxyproject/galaxy/commit/53d387d771b3bb95cd17cf0c74ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Another linting fix. Commit: fed59596a37176b388d74346cd7fce6bba224c8e https://github.com/galaxyproject/galaxy/commit/fed59596a37176b388d74346cd7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix the infinite loop. Thanks @mvdbeek! Commit: 61fb26181c7dfaefa821f616171a281928153b70 https://github.com/galaxyproject/galaxy/commit/61fb26181c7dfaefa821f616171a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/hash_util.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #2840 from mvdbeek/reload_toolbox_across_handlers Allow reloading tools without restarting galaxy, simplify tool panel handling for tool shed installed tools Compare: https://github.com/galaxyproject/galaxy/compare/afefb9dd831f...61fb26181c7d

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[galaxyproject/galaxy] 5483e9: Fix indention for noscratchbook flag
by GitHub 02 Sep '16

02 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5483e9f5bf4d725e3bb2a746db1d9c1a911a5291 https://github.com/galaxyproject/galaxy/commit/5483e9f5bf4d725e3bb2a746db1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix indention for noscratchbook flag Commit: afefb9dd831ff5aed21c74cc159dc6d62eebe64a https://github.com/galaxyproject/galaxy/commit/afefb9dd831ff5aed21c74cc159d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2894 from guerler/revise_noscratchbook_flag Fix indention for noscratchbook flag Compare: https://github.com/galaxyproject/galaxy/compare/cd8daaab1f30...afefb9dd831f

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[galaxyproject/galaxy] b19409: Changed wording on common.mako when selecting how ...
by GitHub 02 Sep '16

02 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1940945607448f3795f98f6ffd8c8dd37c7b3d5 https://github.com/galaxyproject/galaxy/commit/b1940945607448f3795f98f6ffd8… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-09-01 (Thu, 01 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- Changed wording on common.mako when selecting how to install tool and handle dependencies Commit: cd8daaab1f30fd0a45dd4903d0d3de2c9ed5633b https://github.com/galaxyproject/galaxy/commit/cd8daaab1f30fd0a45dd4903d0d3… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-09-02 (Fri, 02 Sep 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- Merge pull request #2893 from nturaga/change_dependency_wording Changed wording on common.mako when selecting how to install tool and… Compare: https://github.com/galaxyproject/galaxy/compare/2b6b5c82754a...cd8daaab1f30

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