August 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 248949: possibility to don't uppercase env variables
by GitHub 18 Aug '17

18 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2489499fb656acc61dc9275931dafcdad381d25c https://github.com/galaxyproject/galaxy/commit/2489499fb656acc61dc9275931da… Author: xgaia <xgaia(a)gmx.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- possibility to don't uppercase env variables Commit: b459399edebbeada2be6254a8567de85b43dabc4 https://github.com/galaxyproject/galaxy/commit/b459399edebbeada2be6254a8567… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #4454 from xgaia/interactive_environment Interactive Environment: possibility to don't uppercase env variables Compare: https://github.com/galaxyproject/galaxy/compare/784e6f5fd360...b459399edebb

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[galaxyproject/galaxy] b8f11d: Improve error message for unknown module types whe...
by GitHub 18 Aug '17

18 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b8f11dfee4efa1d4df47ae3d753af3e9b5c69b82 https://github.com/galaxyproject/galaxy/commit/b8f11dfee4efa1d4df47ae3d753a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Improve error message for unknown module types when encountered. Commit: 213137028182942b372f2483e3b0bb1e20c79518 https://github.com/galaxyproject/galaxy/commit/213137028182942b372f2483e3b0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Print warning if any input connections are unused during workflow execution. Commit: 7bf7f3996373f2528ad7ac88037de3a31f227c23 https://github.com/galaxyproject/galaxy/commit/7bf7f3996373f2528ad7ac88037d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Cleanup a couple things in #4396 caught by @nsoranzo. Commit: 784e6f5fd360f8374045b256171303f5f795264e https://github.com/galaxyproject/galaxy/commit/784e6f5fd360f8374045b2561713… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4396 from jmchilton/workflow_warnings Slightly improve workflow warnings/errors logging. Compare: https://github.com/galaxyproject/galaxy/compare/706741f30b2e...784e6f5fd360

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[galaxyproject/galaxy] 7bab16: Preserve advanced search visibility
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7bab16ef71c850b3cefab3686beeaee3708e1480 https://github.com/galaxyproject/galaxy/commit/7bab16ef71c850b3cefab3686bee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.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.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Preserve advanced search visibility Commit: ee4c8e2afac1d16b386c4dc9afa9b0817a0c9325 https://github.com/galaxyproject/galaxy/commit/ee4c8e2afac1d16b386c4dc9afa9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.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.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix filters Commit: 114997dca6af7483d3ed3f34fafd0f66e3583afc https://github.com/galaxyproject/galaxy/commit/114997dca6af7483d3ed3f34fafd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-view.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.map M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Prevent search tag duplication Commit: 706741f30b2ee0a1733e49cafa8c0d0e6b78385a https://github.com/galaxyproject/galaxy/commit/706741f30b2ee0a1733e49cafa8c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-view.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.map M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge pull request #4449 from guerler/fix_grid_search Fixes for advanced grid search Compare: https://github.com/galaxyproject/galaxy/compare/68e8abc89aba...706741f30b2e

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[galaxyproject/galaxy] 0fa287: Add autopep8 script to help rebasing branches afte...
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0fa287f76a675c49c2702681ac4404f050b77130 https://github.com/galaxyproject/galaxy/commit/0fa287f76a675c49c2702681ac44… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: A .ci/autopep8.sh M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/deletable.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/quota/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/bunch.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/simplegraph.py M lib/galaxy/util/sleeper.py M lib/galaxy/util/ucsc.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/utils.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/request_id.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/middleware/xforwardedhost.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/extract.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M test/casperjs/casperjs_runner.py M test/galaxy_selenium/driver_factory.py M test/shed_functional/functional/test_0060_workflows.py M test/shed_functional/functional/test_0400_repository_component_reviews.py M test/shed_functional/functional/test_0410_repository_component_review_access_control.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1070_invalid_tool.py M tools/data_source/upload.py Log Message: ----------- Add autopep8 script to help rebasing branches after #4440. Fixes a few more PEP8 issues as part of the autopep8'ing as well. Commit: 68e8abc89aba1263f82c643d1bde89da53d70bc9 https://github.com/galaxyproject/galaxy/commit/68e8abc89aba1263f82c643d1bde… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: A .ci/autopep8.sh M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/deletable.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/quota/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/mulled/mulled_search.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/bunch.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/simplegraph.py M lib/galaxy/util/sleeper.py M lib/galaxy/util/ucsc.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/utils.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/request_id.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/middleware/xforwardedhost.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/extract.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M test/casperjs/casperjs_runner.py M test/galaxy_selenium/driver_factory.py M test/shed_functional/functional/test_0060_workflows.py M test/shed_functional/functional/test_0400_repository_component_reviews.py M test/shed_functional/functional/test_0410_repository_component_review_access_control.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1070_invalid_tool.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #4447 from jmchilton/autopep8 Add autopep8 script to help rebasing branches after #4440. Compare: https://github.com/galaxyproject/galaxy/compare/8c225ecf3d92...68e8abc89aba

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[galaxyproject/galaxy] 1e1c54: added missing parameter to function ensure_install...
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e1c549e695cf6541c4dcac5d554c852165e7b6a https://github.com/galaxyproject/galaxy/commit/1e1c549e695cf6541c4dcac5d554… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- added missing parameter to function ensure_installed Commit: a1b8a54ef8009ccf9ac64a699ed848cd56bba283 https://github.com/galaxyproject/galaxy/commit/a1b8a54ef8009ccf9ac64a699ed8… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- ensure_installed is now iterative instead of recursive Commit: 349c9c8f10f6f5eeac45c1a14e3b4a6c23cc373e https://github.com/galaxyproject/galaxy/commit/349c9c8f10f6f5eeac45c1a14e3b… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- version with no repetition at all Commit: a76547281f59b80acd27ddfa098c97e65a72d81a https://github.com/galaxyproject/galaxy/commit/a76547281f59b80acd27ddfa098c… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Set timeout for aquiring lock to 5min Commit: 748539a3a671552eea60e114a6c6e4dd7b48c7de https://github.com/galaxyproject/galaxy/commit/748539a3a671552eea60e114a6c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge pull request #4450 from mvdbeek/fix_file_lock_error [17.01] Fix file lock error handling Commit: 685b9de09bca5a2973de336b93865273c9fa975c https://github.com/galaxyproject/galaxy/commit/685b9de09bca5a2973de336b9386… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into release_17.05 Commit: 8c225ecf3d928b93aceb318dada1e942a510b8ca https://github.com/galaxyproject/galaxy/commit/8c225ecf3d928b93aceb318dada1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-17 (Thu, 17 Aug 2017) Log Message: ----------- Merge branch 'release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7ef099f6a6c9...8c225ecf3d92

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[galaxyproject/galaxy] 1e1c54: added missing parameter to function ensure_install...
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 1e1c549e695cf6541c4dcac5d554c852165e7b6a https://github.com/galaxyproject/galaxy/commit/1e1c549e695cf6541c4dcac5d554… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- added missing parameter to function ensure_installed Commit: a1b8a54ef8009ccf9ac64a699ed848cd56bba283 https://github.com/galaxyproject/galaxy/commit/a1b8a54ef8009ccf9ac64a699ed8… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- ensure_installed is now iterative instead of recursive Commit: 349c9c8f10f6f5eeac45c1a14e3b4a6c23cc373e https://github.com/galaxyproject/galaxy/commit/349c9c8f10f6f5eeac45c1a14e3b… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- version with no repetition at all Commit: a76547281f59b80acd27ddfa098c97e65a72d81a https://github.com/galaxyproject/galaxy/commit/a76547281f59b80acd27ddfa098c… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Set timeout for aquiring lock to 5min Commit: 748539a3a671552eea60e114a6c6e4dd7b48c7de https://github.com/galaxyproject/galaxy/commit/748539a3a671552eea60e114a6c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge pull request #4450 from mvdbeek/fix_file_lock_error [17.01] Fix file lock error handling Commit: 685b9de09bca5a2973de336b93865273c9fa975c https://github.com/galaxyproject/galaxy/commit/685b9de09bca5a2973de336b9386… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/7f78ee7b18b8...685b9de09bca

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[galaxyproject/galaxy] 1e1c54: added missing parameter to function ensure_install...
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 1e1c549e695cf6541c4dcac5d554c852165e7b6a https://github.com/galaxyproject/galaxy/commit/1e1c549e695cf6541c4dcac5d554… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- added missing parameter to function ensure_installed Commit: a1b8a54ef8009ccf9ac64a699ed848cd56bba283 https://github.com/galaxyproject/galaxy/commit/a1b8a54ef8009ccf9ac64a699ed8… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- ensure_installed is now iterative instead of recursive Commit: 349c9c8f10f6f5eeac45c1a14e3b4a6c23cc373e https://github.com/galaxyproject/galaxy/commit/349c9c8f10f6f5eeac45c1a14e3b… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- version with no repetition at all Commit: a76547281f59b80acd27ddfa098c97e65a72d81a https://github.com/galaxyproject/galaxy/commit/a76547281f59b80acd27ddfa098c… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Set timeout for aquiring lock to 5min Commit: 748539a3a671552eea60e114a6c6e4dd7b48c7de https://github.com/galaxyproject/galaxy/commit/748539a3a671552eea60e114a6c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge pull request #4450 from mvdbeek/fix_file_lock_error [17.01] Fix file lock error handling Compare: https://github.com/galaxyproject/galaxy/compare/0f5ad34eaf6b...748539a3a671

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[galaxyproject/galaxy] df442e: Fix E201 errors (spaces in parens) in new memepsp ...
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: df442ea51a05541e83e304432ce4aac678a5b7a9 https://github.com/galaxyproject/galaxy/commit/df442ea51a05541e83e304432ce4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Fix E201 errors (spaces in parens) in new memepsp datatype Commit: 7ef099f6a6c97f0d9ac202860d6873c9a7aed66c https://github.com/galaxyproject/galaxy/commit/7ef099f6a6c97f0d9ac202860d68… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #4446 from dannon/memepsp_formatting Fix E201 errors (spaces in parens) in new memepsp datatype Compare: https://github.com/galaxyproject/galaxy/compare/cca1f9e9bcf4...7ef099f6a6c9

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[galaxyproject/galaxy] 5cebb0: Add support for the MEME psp format
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5cebb086b2849f92ac8da10d7e776e4334c28ff5 https://github.com/galaxyproject/galaxy/commit/5cebb086b2849f92ac8da10d7e77… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.psp Log Message: ----------- Add support for the MEME psp format Commit: 806370123b028eb0728e05fff2f9f9853c5cd6c5 https://github.com/galaxyproject/galaxy/commit/806370123b028eb0728e05fff2f9… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- fix XML error Commit: 7dae650fdbde77336250341832c928f604b41bab https://github.com/galaxyproject/galaxy/commit/7dae650fdbde77336250341832c9… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.memepsp R lib/galaxy/datatypes/test/1.psp Log Message: ----------- Change Psp to MemePsp and misc fixes per initial review Commit: 3026bf56c9662f47062fbd37904803156a4fe0db https://github.com/galaxyproject/galaxy/commit/3026bf56c9662f47062fbd379048… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Remove strange import - no idea from where it originated Commit: 2b94fa3b890a00bbe170ac1bec68d29e8d19c75a https://github.com/galaxyproject/galaxy/commit/2b94fa3b890a00bbe170ac1bec68… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix MemePsp sniff entry Commit: 5799fbc3d13ae6ec41ef5a17e55faf6f58059ae3 https://github.com/galaxyproject/galaxy/commit/5799fbc3d13ae6ec41ef5a17e55f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- change file_ext to be inline with memexml and co Commit: cca1f9e9bcf455b4b655fe9c54707bc34d3c6c32 https://github.com/galaxyproject/galaxy/commit/cca1f9e9bcf455b4b655fe9c5470… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.memepsp Log Message: ----------- Merge pull request #4430 from gregvonkuster/psp_format Add support for the MEME psp format Compare: https://github.com/galaxyproject/galaxy/compare/35ab7457b903...cca1f9e9bcf4

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[galaxyproject/galaxy] 03df49: Fix API tests broken in #4434
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03df496540a6e2099aa4012fb2d46ec44be9bdbf https://github.com/galaxyproject/galaxy/commit/03df496540a6e2099aa4012fb2d4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix API tests broken in #4434 Commit: 35ab7457b9039e9ac6e076ea16bf86dd828faaed https://github.com/galaxyproject/galaxy/commit/35ab7457b9039e9ac6e076ea16bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #4445 from nsoranzo/followup_on_4434 Fix API tests broken in #4434 Compare: https://github.com/galaxyproject/galaxy/compare/a85ee599ffc6...35ab7457b903

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