Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2fce4553d8d0b37cc76a5b12788253f3478b9f14 https://github.com/galaxyproject/galaxy/commit/2fce4553d8d0b37cc76a5b1278825... Author: Pablo Moreno <pcm32@users.noreply.github.com> Date: 2016-06-14 (Tue, 14 Jun 2016) Changed paths: M .ci/py3_sources.txt M client/bower.json R client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/library.less M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/tool_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/config.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py A lib/galaxy/tools/filter_failed_collection.xml A lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/unzip_collection.xml A lib/galaxy/tools/zip_collection.xml M lib/galaxy/util/__init__.py R lib/galaxy/util/directory_hash.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy_utils/sequence/fastq.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/container_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py R static/maps/libs/tracekit.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-select-content.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 R static/scripts/libs/tracekit.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/repair_repository.mako M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/repository/common.mako A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 M test/api/helpers.py M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/interactor.py M test/base/twilltestcase.py A test/functional/tools/exit_code_from_file.xml A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0000_basic_repository_features.py M test/shed_functional/functional/test_1000_install_basic_repository.py M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/workflows/test_run_parameters.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #4 from galaxyproject/dev Stays up-to-date with dev of galaxy project Commit: f3d73f37a2bdb8ed4a46c064243c35658f27a43b https://github.com/galaxyproject/galaxy/commit/f3d73f37a2bdb8ed4a46c064243c3... Author: Pablo Moreno <pablo.a.moreno@gmail.com> Date: 2016-06-14 (Tue, 14 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Removes incorrect FALSE option for include_work_dir which makes certain jobs that discover files from working directories to fail recovering files when running through Kubernetes. Commit: dca91dae163fdcc94aff03920ee75514b7e98a5e https://github.com/galaxyproject/galaxy/commit/dca91dae163fdcc94aff03920ee75... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #2498 from phnmnl/feature/fixFilesFromWorkDirIssue Kubernetes runner: fixes result files from work directory not being recovered issue Compare: https://github.com/galaxyproject/galaxy/compare/1b110299afbf...dca91dae163f