Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f31290113eb1d106b8f1cf894a854c6c310a004 https://github.com/galaxyproject/galaxy/commit/4f31290113eb1d106b8f1cf894a85... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- - get real user name from username and email - sudo calls with preserving PATH, LD_LIBRARY_PATH ... Commit: b07ebdaadaf3d5d4eb089988638f193821015494 https://github.com/galaxyproject/galaxy/commit/b07ebdaadaf3d5d4eb089988638f1... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- - added path check to external chown script Commit: 6841faac692e8b12f7634a547e69ff8a14a9506e https://github.com/galaxyproject/galaxy/commit/6841faac692e8b12f7634a547e69f... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- - removed my paths Commit: d25e552003216d0f986148a161223b010cdcaee8 https://github.com/galaxyproject/galaxy/commit/d25e552003216d0f986148a161223... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- - removed uneccessary import - added quotes to comment Commit: 3a16b36df8471d8c89f5ae04e82199adc3933adf https://github.com/galaxyproject/galaxy/commit/3a16b36df8471d8c89f5ae04e8219... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-05-24 (Wed, 24 May 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- made determination of actual user configurable Commit: 5ee0d7ec0e8d6279be5cbad44d5d41f4d66b317f https://github.com/galaxyproject/galaxy/commit/5ee0d7ec0e8d6279be5cbad44d5d4... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- moved sudo calls to galaxy.ini removed spaces Commit: 01cffa6151f6086c4b944d1146a380d4b0e437da https://github.com/galaxyproject/galaxy/commit/01cffa6151f6086c4b944d1146a38... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- imroved external_chown_script now uses Popen and checks return code Commit: 64f5e2e2fa286bc3cc4151c523d8d98bb4dcf3fe https://github.com/galaxyproject/galaxy/commit/64f5e2e2fa286bc3cc4151c523d8d... Author: rhpvorderman <r.h.p.vorderman@lumc.nl> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py M scripts/external_chown_script.py Log Message: ----------- Fix linting issues Commit: e197cadd98491d8341b3894f5663ea047b2972d2 https://github.com/galaxyproject/galaxy/commit/e197cadd98491d8341b3894f5663e... Author: rhpvorderman <r.h.p.vorderman@lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- fix typo Commit: 71cd8ddcc73744b9e45fc1708be9601f41250dd5 https://github.com/galaxyproject/galaxy/commit/71cd8ddcc73744b9e45fc1708be96... Author: rhpvorderman <r.h.p.vorderman@lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Add system_user_pwent function Commit: 32d7a30943048e43b2700f33c399b6e0ccf2255a https://github.com/galaxyproject/galaxy/commit/32d7a30943048e43b2700f33c399b... Author: rhpvorderman <r.h.p.vorderman@lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Add system_user_pwent function to upload and jobs Commit: 2ec805417c6a251319714178e5be088cc285ebc9 https://github.com/galaxyproject/galaxy/commit/2ec805417c6a251319714178e5be0... Author: rhpvorderman <r.h.p.vorderman@lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- Change paramter typo Commit: e81a2ac65454e0dd88d474210036d166c3055a5b https://github.com/galaxyproject/galaxy/commit/e81a2ac65454e0dd88d474210036d... Author: rhpvorderman <r.h.p.vorderman@lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- Fix removed duplication in external chown script Commit: c275d25be9873e259777506e46b6f7989213e172 https://github.com/galaxyproject/galaxy/commit/c275d25be9873e259777506e46b6f... Author: rhpvorderman <r.h.p.vorderman@lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- Fix linting Commit: aa200fe46351eaa6f7ab30899cdf57bdaa2b069a https://github.com/galaxyproject/galaxy/commit/aa200fe46351eaa6f7ab30899cdf5... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/upload_common.py M scripts/external_chown_script.py Log Message: ----------- implemented the changes requested by @mvdbeek: - check for external_chown_script == None - switched from string split to shlex.split - changed import order for pwd - stderr + exit -> just exit Commit: e8f44de501dec8b04864b574687d8098ea3bab1e https://github.com/galaxyproject/galaxy/commit/e8f44de501dec8b04864b574687d8... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- bugfix missing colon Commit: ae1903d396584fe51bf77127b84ea7cf7b831fb6 https://github.com/galaxyproject/galaxy/commit/ae1903d396584fe51bf77127b84ea... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- shlex.split also for external kill and run scripts Commit: 7fbd3f2bc229d60da22535b062465b1794e39335 https://github.com/galaxyproject/galaxy/commit/7fbd3f2bc229d60da22535b062465... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- added missing empty line Commit: 074b90d55edc0a82115aac3adc5b189e7144c0b3 https://github.com/galaxyproject/galaxy/commit/074b90d55edc0a82115aac3adc5b1... Author: bernt@informatik.uni-leipzig.de <bernt@informatik.uni-leipzig.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/model/__init__.py M scripts/external_chown_script.py Log Message: ----------- bug fixes - system_user_pwent: undefined return value when KeyError - external_chown_script: * typo * subprocess instead of os.subprocess Commit: f83871d0707dea0256a5f409f285eec16f7bcef7 https://github.com/galaxyproject/galaxy/commit/f83871d0707dea0256a5f409f285e... Author: bernt@informatik.uni-leipzig.de <bernt@informatik.uni-leipzig.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/runners/drmaa.py M scripts/drmaa_external_runner.py Log Message: ----------- moved assign_all_groups parameter to config Commit: 351adc6574dce1e0be8f3e079a84b77f46f045f6 https://github.com/galaxyproject/galaxy/commit/351adc6574dce1e0be8f3e079a84b... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M CONTRIBUTORS.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js A client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/dev/build_a_job_runner.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst A doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.galaxy.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst M doc/source/lib/galaxy.webapps.tool_shed.framework.rst M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst M doc/source/lib/galaxy.webapps.tool_shed.model.rst M doc/source/lib/galaxy.webapps.tool_shed.rst M doc/source/lib/galaxy.webapps.tool_shed.search.rst M doc/source/lib/galaxy.webapps.tool_shed.security.rst M doc/source/lib/galaxy.webapps.tool_shed.util.rst A doc/source/lib/galaxy.webhooks.rst M doc/source/lib/galaxy.work.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/galaxy.workflow.schedulers.rst M doc/source/lib/galaxy_ext.metadata.rst M doc/source/lib/galaxy_ext.rst M doc/source/lib/log_tempfile.rst M doc/source/lib/psyco_full.rst M doc/source/lib/tool_shed.capsule.rst M doc/source/lib/tool_shed.dependencies.repository.rst M doc/source/lib/tool_shed.dependencies.rst M doc/source/lib/tool_shed.dependencies.tool.rst M doc/source/lib/tool_shed.galaxy_install.datatypes.rst M doc/source/lib/tool_shed.galaxy_install.grids.rst M doc/source/lib/tool_shed.galaxy_install.metadata.rst M doc/source/lib/tool_shed.galaxy_install.migrate.rst M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst M doc/source/lib/tool_shed.galaxy_install.tools.rst M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst M doc/source/lib/tool_shed.grids.rst M doc/source/lib/tool_shed.managers.rst M doc/source/lib/tool_shed.metadata.rst M doc/source/lib/tool_shed.repository_types.rst M doc/source/lib/tool_shed.rst M doc/source/lib/tool_shed.tools.rst M doc/source/lib/tool_shed.util.rst M doc/source/lib/tool_shed.utility_containers.rst M doc/source/releases/13.01_announce.rst M doc/source/releases/13.02_announce.rst M doc/source/releases/13.04_announce.rst M doc/source/releases/13.06_announce.rst M doc/source/releases/13.08_announce.rst M doc/source/releases/13.11_announce.rst M doc/source/releases/14.02_announce.rst M doc/source/releases/14.04_announce.rst M doc/source/releases/14.06_announce.rst M doc/source/releases/14.08_announce.rst M doc/source/releases/14.10_announce.rst M doc/source/releases/15.01_announce.rst M doc/source/releases/15.03_announce.rst M doc/source/releases/15.05.rst M doc/source/releases/15.05_announce.rst M doc/source/releases/15.07_announce.rst M doc/source/releases/15.10_announce.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07_announce.rst M doc/source/releases/16.10_announce.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/releases/older_releases.rst M doc/source/slideshow/architecture/galaxy_architecture.md M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/cache.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/mulled/util.py A lib/galaxy/tools/deps/singularity_util.py M lib/galaxy/tools/parameters/__init__.py R lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/compression_utils.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_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/metadata/metadata_generator.py M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map A static/maps/mvc/page/page-list.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-slider.js.map A static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/layout/menu.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js A static/scripts/mvc/page/page-list.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-slider.js A static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M static/welcome.html.sample M templates/grid_base.mako M templates/sharing_base.mako R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako R templates/webapps/galaxy/page/list_published.mako R templates/webapps/galaxy/workflow/configure_menu.mako M test/api/test_dataset_collections.py M test/base/populators.py A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 57c112442d53dfff5cc9be9c775fd81eb7cae03d https://github.com/galaxyproject/galaxy/commit/57c112442d53dfff5cc9be9c775fd... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- fixed typos in galaxy.ini Commit: 698075c3d7fa5745cc437d36a9c0c48e3f0c6f9f https://github.com/galaxyproject/galaxy/commit/698075c3d7fa5745cc437d36a9c0c... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/webapps/galaxy/api/webhooks.py M scripts/api/library_upload_dir.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.js.map M static/maps/onload.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 M static/scripts/layout/menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 153b8d4dca041f43d704cab052b1b733d74658c8 https://github.com/galaxyproject/galaxy/commit/153b8d4dca041f43d704cab052b1b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/upload_common.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py Log Message: ----------- Merge pull request #4096 from bernt-matthias/dev get real user name from username and email (for submission as real user with drmaa) Compare: https://github.com/galaxyproject/galaxy/compare/a57b4c171525...153b8d4dca04