Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5071b698718caae30115f463a184aa76f2017250 https://github.com/galaxyproject/galaxy/commit/5071b698718caae30115f463a184a... Author: Jelle Scholtalbers <j.scholtalbers@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/74e551d34cfb5bb50ca061f682de9... Author: Jelle Scholtalbers <j.scholtalbers@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/ae3afae8f002fccb1b236271da420... Author: Jelle Scholtalbers <j.scholtalbers@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/8553ea2c6e9fedb88579f1a7e9e87... Author: Jelle Scholtalbers <j.scholtalbers@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/729b0bf63b2990849809f32da45ef... Author: Jelle Scholtalbers <j.scholtalbers@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/4947ab0738a076ef7cc60856271a1... Author: Jelle Scholtalbers <j.scholtalbers@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/ea7dbd1906bc612804448fd94af05... Author: Nate Coraor <nate@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/ebafd19575ba4898da9ed237683a7... Author: Nate Coraor <nate@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