galaxy-commits January 2018

galaxy-commits@lists.galaxyproject.org

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115 discussions

[galaxyproject/galaxy] 6e865a: Environment variable to skip client build.
by GitHub 24 Jan '18

24 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e865a3363587582165788ea7b604cda084dff4f https://github.com/galaxyproject/galaxy/commit/6e865a3363587582165788ea7b60… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Environment variable to skip client build. Need to fix https://github.com/galaxyproject/planemo/issues/750 but I don't want to send along command-line arguments that will break older Galaxies, better just to set an environment variable that will be ignored for older Galaxies I think. Commit: dd88194e8f5690cc390c60008934dfff341ed047 https://github.com/galaxyproject/galaxy/commit/dd88194e8f5690cc390c60008934… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5371 from jmchilton/environment_client_skip Environment variable to skip client build. Compare: https://github.com/galaxyproject/galaxy/compare/a4154a13c9ea...dd88194e8f56

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[galaxyproject/galaxy] 5092dd: Fix logic in deactivate or uninstall
by GitHub 23 Jan '18

23 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5092ddf3f565f4b361bc37a3afea6959e0c801e6 https://github.com/galaxyproject/galaxy/commit/5092ddf3f565f4b361bc37a3afea… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako Log Message: ----------- Fix logic in deactivate or uninstall The form value interpreter no longer uses `['true', 'true']` to determine whether a checkbox is checked, so a single form value of 'true' will now be sufficient. Commit: a4154a13c9ea1211d470782820fcdab40a898829 https://github.com/galaxyproject/galaxy/commit/a4154a13c9ea1211d470782820fc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako Log Message: ----------- Merge pull request #5363 from galaxyproject/uninstall_repo_fix Fix logic in deactivate or uninstall Compare: https://github.com/galaxyproject/galaxy/compare/135328fff04a...a4154a13c9ea

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[galaxyproject/galaxy] 5092dd: Fix logic in deactivate or uninstall
by GitHub 23 Jan '18

23 Jan '18

Branch: refs/heads/uninstall_repo_fix Home: https://github.com/galaxyproject/galaxy Commit: 5092ddf3f565f4b361bc37a3afea6959e0c801e6 https://github.com/galaxyproject/galaxy/commit/5092ddf3f565f4b361bc37a3afea… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako Log Message: ----------- Fix logic in deactivate or uninstall The form value interpreter no longer uses `['true', 'true']` to determine whether a checkbox is checked, so a single form value of 'true' will now be sufficient.

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[galaxyproject/galaxy] e7e87c: Handle case when no user is attached to the job
by GitHub 23 Jan '18

23 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e7e87c31c80eaaedbee20735702efa0c8e343655 https://github.com/galaxyproject/galaxy/commit/e7e87c31c80eaaedbee20735702e… Author: E Rasche <hxr(a)hx42.org> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Handle case when no user is attached to the job Commit: 135328fff04aab13a21b2416ccd6867d58cd0b29 https://github.com/galaxyproject/galaxy/commit/135328fff04aab13a21b2416ccd6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #5358 from erasche/job-info-no-user Handle none job owner in API Compare: https://github.com/galaxyproject/galaxy/compare/84ae5db0f195...135328fff04a

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[galaxyproject/usegalaxy-playbook] e0e90e: Test mutable configs
by GitHub 22 Jan '18

22 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e0e90e00fc22d87eac6499c3f907c0074160d68a https://github.com/galaxyproject/usegalaxy-playbook/commit/e0e90e00fc22d87e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs

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[galaxyproject/galaxy] 40a5dd: fix image proxy prefix in tool form
by GitHub 22 Jan '18

22 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 40a5ddde01f5b1b88f64950c448b50f18ec27509 https://github.com/galaxyproject/galaxy/commit/40a5ddde01f5b1b88f64950c448b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- fix image proxy prefix in tool form alternatively I think this could be fixed at the point when this image url is being generated on backend Commit: cb9fe3efe893ed45db6ba33cfcdb9b977b4703de https://github.com/galaxyproject/galaxy/commit/cb9fe3efe893ed45db6ba33cfcdb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- implement more restrictive selector, use jquery each isntead of _ thanks to jmchilton and dannon Commit: 5554c2f9b98b4192e106fdce52fa067945f431e8 https://github.com/galaxyproject/galaxy/commit/5554c2f9b98b4192e106fdce52fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Fix import by url for history archive import tool Commit: b82676b8eec35313896614aa0fb5fdeeddacf541 https://github.com/galaxyproject/galaxy/commit/b82676b8eec35313896614aa0fb5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py Log Message: ----------- Switch to transparent readmode for history tarfiles Commit: b5d0030b3ed4bf08aa26c29b72c4f5757874669c https://github.com/galaxyproject/galaxy/commit/b5d0030b3ed4bf08aa26c29b72c4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix history import by file on multi-handler setups The uploaded archive was going to be deleted before the job started running. Commit: 662440e730791318b5ff3a9346f1ee6243c56208 https://github.com/galaxyproject/galaxy/commit/662440e730791318b5ff3a9346f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml Log Message: ----------- Add quotes Commit: 8fa785427cf8d41fd420092baaaf574825bb9d0b https://github.com/galaxyproject/galaxy/commit/8fa785427cf8d41fd420092baaaf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5344 from mvdbeek/history_import_fixes [17.09] History import fixes Commit: 0fdb63e5e327ef6b82c928004b5e3301967f9eb3 https://github.com/galaxyproject/galaxy/commit/0fdb63e5e327ef6b82c928004b5e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- remove charlimit for fetching urls fixes #5349 this would only allow a number of urls that fit 1024 chars together moreover it would truncate (and break) the last one Commit: 3bf9b3ab1d718d5ecd02f7539015c5328d6c72ef https://github.com/galaxyproject/galaxy/commit/3bf9b3ab1d718d5ecd02f7539015… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #5353 from martenson/remove-charlimit-for-fetch [17.09] remove charlimit for fetching urls Commit: 4288e96b77fc77c5409e499bf92ba880a6dcbe4d https://github.com/galaxyproject/galaxy/commit/4288e96b77fc77c5409e499bf92b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #5237 from martenson/fix-image-proxy-prefix [17.05] fix image proxy prefix in tool form Commit: 177aa2e7f994afc9f2749603e6d1ad20c9ffea77 https://github.com/galaxyproject/galaxy/commit/177aa2e7f994afc9f2749603e6d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 7996a4c0c73eb53774b2d871f496e36b9a6ec54a https://github.com/galaxyproject/galaxy/commit/7996a4c0c73eb53774b2d871f496… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Rebuild client for stable 17.09 Commit: 0e0303743dcb305bd2c3ea66f80b3be9ebdcd351 https://github.com/galaxyproject/galaxy/commit/0e0303743dcb305bd2c3ea66f80b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge branch 'release_17.09' into dev Commit: 84ae5db0f195adcbbb1a1074d6cc6d0729f1598a https://github.com/galaxyproject/galaxy/commit/84ae5db0f195adcbbb1a1074d6cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Client formatting Compare: https://github.com/galaxyproject/galaxy/compare/ebafd19575ba...84ae5db0f195

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[galaxyproject/galaxy] 40a5dd: fix image proxy prefix in tool form
by GitHub 22 Jan '18

22 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 40a5ddde01f5b1b88f64950c448b50f18ec27509 https://github.com/galaxyproject/galaxy/commit/40a5ddde01f5b1b88f64950c448b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- fix image proxy prefix in tool form alternatively I think this could be fixed at the point when this image url is being generated on backend Commit: cb9fe3efe893ed45db6ba33cfcdb9b977b4703de https://github.com/galaxyproject/galaxy/commit/cb9fe3efe893ed45db6ba33cfcdb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- implement more restrictive selector, use jquery each isntead of _ thanks to jmchilton and dannon Commit: 4288e96b77fc77c5409e499bf92ba880a6dcbe4d https://github.com/galaxyproject/galaxy/commit/4288e96b77fc77c5409e499bf92b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #5237 from martenson/fix-image-proxy-prefix [17.05] fix image proxy prefix in tool form Commit: 177aa2e7f994afc9f2749603e6d1ad20c9ffea77 https://github.com/galaxyproject/galaxy/commit/177aa2e7f994afc9f2749603e6d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 7996a4c0c73eb53774b2d871f496e36b9a6ec54a https://github.com/galaxyproject/galaxy/commit/7996a4c0c73eb53774b2d871f496… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Rebuild client for stable 17.09 Compare: https://github.com/galaxyproject/galaxy/compare/3bf9b3ab1d71...7996a4c0c73e

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[galaxyproject/galaxy] 40a5dd: fix image proxy prefix in tool form
by GitHub 22 Jan '18

22 Jan '18

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 40a5ddde01f5b1b88f64950c448b50f18ec27509 https://github.com/galaxyproject/galaxy/commit/40a5ddde01f5b1b88f64950c448b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- fix image proxy prefix in tool form alternatively I think this could be fixed at the point when this image url is being generated on backend Commit: cb9fe3efe893ed45db6ba33cfcdb9b977b4703de https://github.com/galaxyproject/galaxy/commit/cb9fe3efe893ed45db6ba33cfcdb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- implement more restrictive selector, use jquery each isntead of _ thanks to jmchilton and dannon Commit: 4288e96b77fc77c5409e499bf92ba880a6dcbe4d https://github.com/galaxyproject/galaxy/commit/4288e96b77fc77c5409e499bf92b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #5237 from martenson/fix-image-proxy-prefix [17.05] fix image proxy prefix in tool form Compare: https://github.com/galaxyproject/galaxy/compare/d1510c739492...4288e96b77fc

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[galaxyproject/galaxy] 5071b6: Add option to auto create user_library_import_dir ...
by GitHub 22 Jan '18

22 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5071b698718caae30115f463a184aa76f2017250 https://github.com/galaxyproject/galaxy/commit/5071b698718caae30115f463a184… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Add option to auto create user_library_import_dir directories upon user login. Commit: 74e551d34cfb5bb50ca061f682de97084ade5a2e https://github.com/galaxyproject/galaxy/commit/74e551d34cfb5bb50ca061f682de… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- one less variable.. Commit: ae3afae8f002fccb1b236271da4204b1115eef23 https://github.com/galaxyproject/galaxy/commit/ae3afae8f002fccb1b236271da42… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- sort import order alphabetically Commit: 8553ea2c6e9fedb88579f1a7e9e8727fc2a977a7 https://github.com/galaxyproject/galaxy/commit/8553ea2c6e9fedb88579f1a7e9e8… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- move logic to webapps.py Commit: 729b0bf63b2990849809f32da45ef078d206069b https://github.com/galaxyproject/galaxy/commit/729b0bf63b2990849809f32da45e… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- fix toolshed test with missing config attribute Commit: 4947ab0738a076ef7cc60856271a1585c259fa36 https://github.com/galaxyproject/galaxy/commit/4947ab0738a076ef7cc60856271a… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- use safemakedirs instead of private _ensure_directory Commit: ea7dbd1906bc612804448fd94af05e7812c60e38 https://github.com/galaxyproject/galaxy/commit/ea7dbd1906bc612804448fd94af0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tours.js M config/datatypes_conf.xml.sample R config/galaxy.ini.sample A config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/histories.py A lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh A scripts/common_startup_variables.sh M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_uwsgi_args.py A scripts/maintenance.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M templates/webapps/galaxy/history/display_structured.mako A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/base/driver_util.py M test/base/integration_util.py M test/docker/base/run_test_wrapper.sh A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/multi_output_recurse.xml A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/integration/dockerized_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M tools/data_source/microbial_import_code.py Log Message: ----------- Merge remote-tracking branch 'origin/dev' into feature/auto_create_userfolder Commit: ebafd19575ba4898da9ed237683a76f8d3be7000 https://github.com/galaxyproject/galaxy/commit/ebafd19575ba4898da9ed237683a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5138 from scholtalbers/feature/auto_create_userfolder Add option to auto create user_library_import_dir directories upon user login Compare: https://github.com/galaxyproject/galaxy/compare/e14dde16fb9a...ebafd19575ba

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[galaxyproject/galaxy] 208dcb: Stop walking up to parent HDA
by GitHub 21 Jan '18

21 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 208dcb9196466af1db363d4b307391d5ad36e042 https://github.com/galaxyproject/galaxy/commit/208dcb9196466af1db363d4b3073… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Stop walking up to parent HDA Commit: ca51898bc4038fc93fa53a5a2fa9367ab8db6b8b https://github.com/galaxyproject/galaxy/commit/ca51898bc4038fc93fa53a5a2fa9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M scripts/cleanup_datasets/cleanup_datasets.py Log Message: ----------- Fix cleanup datasets script Commit: 654ed86b376f0b7492f2f4370a4e6a903a15d37f https://github.com/galaxyproject/galaxy/commit/654ed86b376f0b7492f2f4370a4e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M scripts/db_shell.py Log Message: ----------- Setup a dummy registry to allow some more operations, e.g. accessing metadata Commit: 89d45416fbb75d10ad43940308bd2e0dc4d2ede2 https://github.com/galaxyproject/galaxy/commit/89d45416fbb75d10ad43940308bd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M scripts/cleanup_datasets/cleanup_datasets.py Log Message: ----------- Import Registry directly Commit: e14dde16fb9ab4175f9a8f252eb4e7249dbb6d4f https://github.com/galaxyproject/galaxy/commit/e14dde16fb9ab4175f9a8f252eb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-21 (Sun, 21 Jan 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/db_shell.py Log Message: ----------- Merge pull request #5346 from mvdbeek/fix_hda_parent_access Fix dataset purging, dataset cleanup script and db_shell script Compare: https://github.com/galaxyproject/galaxy/compare/5be96485b5a7...e14dde16fb9a

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