- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 12a789: Adjust tests for 8cca7be
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 12a789f3e19c7ac02f9648461cb2cd3dbd2727eb https://github.com/galaxyproject/galaxy/commit/12a789f3e19c7ac02f9648461cb2… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Adjust tests for 8cca7be Commit: fed3665fcfa96809a00fb4d9b4dfe287123d84f3 https://github.com/galaxyproject/galaxy/commit/fed3665fcfa96809a00fb4d9b4df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Merge pull request #2680 from mvdbeek/toolshed_test_fixes Fix broken toolshed tests with #2554 Compare: https://github.com/galaxyproject/galaxy/compare/c7caeb3c3959...fed3665fcfa9

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[galaxyproject/galaxy] ea36a6: first commit
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea36a627e48d71a5ef3482be36d64b3a57c10235 https://github.com/galaxyproject/galaxy/commit/ea36a627e48d71a5ef3482be36d6… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: A lib/galaxy/objectstore/azureObjectStore.py Log Message: ----------- first commit modeled off S3 adapter Commit: 596248ae0f2af5cb1a01dbb8de8f05c572c4bbcb https://github.com/galaxyproject/galaxy/commit/596248ae0f2af5cb1a01dbb8de8f… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/graphviz/static/js/graphVis.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/visualizations/graphviz/templates/graphviz.mako M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.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/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js M templates/admin/impersonate.mako M templates/ind_share_base.mako M test/api/test_users.py M test/unit/managers/test_UserManager.py M tools/stats/gsummary.xml Log Message: ----------- Merge branch 'dev' into azure-blob-objectstore Commit: c3a074faf044fa21e73ae060e4d5a1872d8b9475 https://github.com/galaxyproject/galaxy/commit/c3a074faf044fa21e73ae060e4d5… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M config/object_store_conf.xml.sample Log Message: ----------- added object_store_conf.xml.sample Commit: b217ecde14d80f211bc550cb56fa4524872e23f9 https://github.com/galaxyproject/galaxy/commit/b217ecde14d80f211bc550cb56fa… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/tool/tool-form-composite.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/mvc/tool/tool-form-composite.js A test/unit/datatypes/test_data.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: 0a49f17411dec1235226a8dc0fc7237bc4f6a40a https://github.com/galaxyproject/galaxy/commit/0a49f17411dec1235226a8dc0fc7… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M doc/source/lib/galaxy.objectstore.rst Log Message: ----------- Modified galaxy.objectstore.rst Not sure how RST works — would appreciate some guidance here. Commit: 3a3074134fd0bbdf81c269e127934d1c87b0d8bd https://github.com/galaxyproject/galaxy/commit/3a3074134fd0bbdf81c269e12793… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azureObjectStore.py Log Message: ----------- fixed most lint errors Commit: cb44eb372ef71d856804c3747e0e282e14176702 https://github.com/galaxyproject/galaxy/commit/cb44eb372ef71d856804c3747e0e… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/job_conf.xml.sample_advanced A config/tool_destinations.yml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/history/grid.mako M test/api/test_workflows.py A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/stats/gsummary.xml Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: c668baeea5d4106e439ebbb39d406ccc1f4848f2 https://github.com/galaxyproject/galaxy/commit/c668baeea5d4106e439ebbb39d40… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: R lib/galaxy/objectstore/azureObjectStore.py A lib/galaxy/objectstore/azure_blob.py Log Message: ----------- better naming Commit: 8bc8e38b369115d9970586a24626d04b101c6952 https://github.com/galaxyproject/galaxy/commit/8bc8e38b369115d9970586a24626… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- typo Commit: 4fa0c27bf1594a3f46209e3718d55fd7063bbbd9 https://github.com/galaxyproject/galaxy/commit/4fa0c27bf1594a3f46209e3718d5… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Another lint pass. Commit: 2405f558c8d3abc0cbbe1738208e682d9bc02502 https://github.com/galaxyproject/galaxy/commit/2405f558c8d3abc0cbbe1738208e… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Oops.. Commit: a2c5e33d021f61b0e2efa95b12fc6a9d3e7ae82e https://github.com/galaxyproject/galaxy/commit/a2c5e33d021f61b0e2efa95b12fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Address minor azure objblob lint issues, and one UndefinedObject issue. Commit: ebe83e21bd25c5fc9d4c4f8018401e5967d5cd66 https://github.com/galaxyproject/galaxy/commit/ebe83e21bd25c5fc9d4c4f801840… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge pull request #1 from dannon/minor_azure_tweaks Address minor azure objblob lint issues, and one UndefinedObject issue. Commit: d9d549299171364576e141710637283176fd6dd4 https://github.com/galaxyproject/galaxy/commit/d9d549299171364576e141710637… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/object_store_conf.xml.sample Log Message: ----------- more consistent naming. Commit: 4a8a14d8cf593b84cc338062d7361140f8410851 https://github.com/galaxyproject/galaxy/commit/4a8a14d8cf593b84cc338062d736… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: ca79c905f83aa20be3a598da94ec09919457511a https://github.com/galaxyproject/galaxy/commit/ca79c905f83aa20be3a598da94ec… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- oops again... Commit: 91081bf2802195f501595bca9a51b38b69c18669 https://github.com/galaxyproject/galaxy/commit/91081bf2802195f501595bca9a51… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- added dependency to azure Commit: 7dcc6374ccf9ce9903cc82f11f146a1f5aefdc87 https://github.com/galaxyproject/galaxy/commit/7dcc6374ccf9ce9903cc82f11f14… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- oops =) Commit: d36162a389586ffa0d692a446be26c53b1e7741d https://github.com/galaxyproject/galaxy/commit/d36162a389586ffa0d692a446be2… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- fixes the lint error I think. Commit: e59602fed14e0f7bea81309407e47e600a24a529 https://github.com/galaxyproject/galaxy/commit/e59602fed14e0f7bea81309407e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Update check_azure_storage check, read the object store config to detect stores. Commit: 3199217448f7646c660c954c66e989f4a2e224fb https://github.com/galaxyproject/galaxy/commit/3199217448f7646c660c954c66e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Remove debug print Commit: 0da66864e491e7b8b1a5454ee12a3db1ba52e9e1 https://github.com/galaxyproject/galaxy/commit/0da66864e491e7b8b1a5454ee12a… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Merge pull request #2 from dannon/azure-blob-objectstore Fixes azure_blob detection for conditional dependency resolution Commit: 0b1730fe7f94875edf378dec629f692da66c8ad3 https://github.com/galaxyproject/galaxy/commit/0b1730fe7f94875edf378dec629f… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- trying this... Commit: e349aafe047ce0e419634b96c34acef8b60549af https://github.com/galaxyproject/galaxy/commit/e349aafe047ce0e419634b96c34a… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- fix bug. Commit: 4dc8b7d8037defe9b29038ee05ab22b889cd2740 https://github.com/galaxyproject/galaxy/commit/4dc8b7d8037defe9b29038ee05ab… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- clean things up a little... Commit: b4896bc341ab9d40a255c74a7a5fdeb0db37f72a https://github.com/galaxyproject/galaxy/commit/b4896bc341ab9d40a255c74a7a5f… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- fix lint Commit: c7caeb3c3959e87e55e791aa4f87de63e71a9032 https://github.com/galaxyproject/galaxy/commit/c7caeb3c3959e87e55e791aa4f87… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M config/object_store_conf.xml.sample M doc/source/lib/galaxy.objectstore.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge branch 'azure-blob-objectstore' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c4841b352140...c7caeb3c3959

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[galaxyproject/galaxy] 43f800: Modify persistent entry handling for select fields
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43f800b56d3002248e42b4145df272a2ad572a7f https://github.com/galaxyproject/galaxy/commit/43f800b56d3002248e42b4145df2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Modify persistent entry handling for select fields Commit: 3dcc9adaaffa032e1adb57a42e9054ef8ddfe958 https://github.com/galaxyproject/galaxy/commit/3dcc9adaaffa032e1adb57a42e90… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form.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.js Log Message: ----------- Improve robustness of error message display on tool execution Commit: b9a02150fef9007391e79521b0712f898ed657b9 https://github.com/galaxyproject/galaxy/commit/b9a02150fef9007391e79521b071… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-default.js Log Message: ----------- Filter on the basis of select field values instead of all attributes Commit: c4841b35214083a9cabb51fd816fe7fac3d53684 https://github.com/galaxyproject/galaxy/commit/c4841b35214083a9cabb51fd816f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #2677 from guerler/update_select Fix dataset selector update when deleting history items Compare: https://github.com/galaxyproject/galaxy/compare/d7a1776a9105...c4841b352140

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[galaxyproject/galaxy] 497afd: Fix config.dynamic_proxy.
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 497afd86a6e4110d74b0caefe5e40f86baf257cd https://github.com/galaxyproject/galaxy/commit/497afd86a6e4110d74b0caefe5e4… Author: thoba <lose.thoba(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M .gitignore A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Fix config.dynamic_proxy. Commit: a188c1019749200da93b77401e098e978bdf7572 https://github.com/galaxyproject/galaxy/commit/a188c1019749200da93b77401e09… Author: thoba <lose.thoba(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Minor IE updates. Commit: 6732bea22dbd67b8f3ad02c81310bcb69549ec2d https://github.com/galaxyproject/galaxy/commit/6732bea22dbd67b8f3ad02c81310… Author: thoba <lose.thoba(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M .ci/py3_sources.txt M Makefile M README.rst M client/bower.json M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.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 R client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-frames.js M 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test/unit/web/framework/test_webapp.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 M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.xml M tools/filters/axt_to_fasta.xml M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav.xml M tools/filters/bed2gff.xml M tools/filters/bed_to_bigbed.xml M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff2bed.xml M tools/filters/gff_to_bed_converter.py M tools/filters/gtf2bedgraph.xml M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M 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tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Commit: 4ae93fc0f2f3963a138947511db48febf71d37fc https://github.com/galaxyproject/galaxy/commit/4ae93fc0f2f3963a138947511db4… Author: thoba <lose.thoba(a)gmail.com> Date: 2016-07-13 (Wed, 13 Jul 2016) Changed paths: M .gitignore M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/templates/neo.mako M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Removed extra proxy_command arg Added Newline Commit: 23f8aab6c6f462b4a343101bd95ed46a63005d16 https://github.com/galaxyproject/galaxy/commit/23f8aab6c6f462b4a343101bd95e… Author: thoba <lose.thoba(a)gmail.com> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M config/plugins/interactive_environments/neo/config/neo.ini.sample Log Message: ----------- Default to internals. Commit: 79b325403094942dfde7d62afeab5a426d6259aa https://github.com/galaxyproject/galaxy/commit/79b325403094942dfde7d62afeab… Author: Thoba Lose <thobalose(a)users.noreply.github.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample Log Message: ----------- Added Docker image tag Commit: d7a1776a91051b70d2be08b04681083053419cb4 https://github.com/galaxyproject/galaxy/commit/d7a1776a91051b70d2be08b04681… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Merge pull request #2610 from thobalose/dev Added Neo4j IE Compare: https://github.com/galaxyproject/galaxy/compare/a731ce2e2225...d7a1776a9105

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[galaxyproject/galaxy] fd9eb8: WIP re #39 - run dependency management during repo...
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd9eb822b470dfedc508511ae27e79fd02f317b3 https://github.com/galaxyproject/galaxy/commit/fd9eb822b470dfedc508511ae27e… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- WIP re #39 - run dependency management during repository installation working: - fetching valid tool list - identifying unique requirements not working: File '/Users/langhorst/src/galaxy_hackathon/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1138 in prepare_for_install [view.manager_dependency(req) for req in uniq_reqs.values()] TypeError: manager_dependency() takes exactly 1 argument (2 given) Commit: dcb57a6f17f5f351d585bb2b0535c0f0c04c9f4f https://github.com/galaxyproject/galaxy/commit/dcb57a6f17f5f351d585bb2b0535… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Need to unnpack kwargs (ping @bwlang) Commit: de6bbf1f755ac6659ff733146a396013cebbf231 https://github.com/galaxyproject/galaxy/commit/de6bbf1f755ac6659ff733146a39… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Move get_unique_requirements to shed_util_common (ping @bwlang) Commit: 179d02c701ad92902ec7c718a4c453de1fff858b https://github.com/galaxyproject/galaxy/commit/179d02c701ad92902ec7c718a4c4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Iterate over all tools in a repository Commit: f7d5f5d1912c46fa024bd61adedbee3e7f059a03 https://github.com/galaxyproject/galaxy/commit/f7d5f5d1912c46fa024bd61adedb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix the parsing logic Commit: 07ed963d8b4cac3ebec3af1289908eb6566b8b11 https://github.com/galaxyproject/galaxy/commit/07ed963d8b4cac3ebec3af128990… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Be a bit more defensive about parsing requirements Commit: f0f6d88e34ece5e083e960e1cf1d2eb750226feb https://github.com/galaxyproject/galaxy/commit/f0f6d88e34ece5e083e960e1cf1d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix indentation Commit: e7aaf99392c95ded8f620adc2827700c1a3d3f2a https://github.com/galaxyproject/galaxy/commit/e7aaf99392c95ded8f620adc2827… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- passed a “manual install” argument to the dependency resolve so that we can both respect a users wishes (independent of auto_install config) and so that we can avoid attempting to create a conda_env in a nonexistent job directory Commit: 523baf380fe5798e3838480f802feda582361746 https://github.com/galaxyproject/galaxy/commit/523baf380fe5798e3838480f802f… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Probably better not to have a fake directory here… other places check for job_directory=None Commit: 0252acce55f32c2751570547c4ddc4548e5d29c1 https://github.com/galaxyproject/galaxy/commit/0252acce55f32c2751570547c4dd… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- ask for tool dependency installation always. I think a tool with no requirements is probably rare, and the new language should cover that situation. I think it’s not worth the API call to fetch the requirements just to ask this question. Commit: dade96c4af3a265010fd068e3d9562612996aff7 https://github.com/galaxyproject/galaxy/commit/dade96c4af3a265010fd068e3d95… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- this view is not necessary for the current implementation Commit: 609898b73c8a11412b110c0e6370617a95cf3a89 https://github.com/galaxyproject/galaxy/commit/609898b73c8a11412b110c0e6370… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- strangely… we need %if tool_dependencies_root_folder or missing_tool_dependencies_root_folder: to avoid breaking the export repository code Commit: c59fd5ec955c853f8306622d669a095562ed6350 https://github.com/galaxyproject/galaxy/commit/c59fd5ec955c853f8306622d669a… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- resolving style issue better comments Commit: 753587931ed3a460e57334de398d5048bc35f6b9 https://github.com/galaxyproject/galaxy/commit/753587931ed3a460e57334de398d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/requirements.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add api route to fetch all requirements and method that determines requirement status This should be used in the UI to inform the admin of the dependency resolution status. Also make galaxy package resolution more robust to other files in the shed_tools directory (like condarc). Commit: 1a9e2e72663902287a2963464d38894aa6f8e4aa https://github.com/galaxyproject/galaxy/commit/1a9e2e72663902287a2963464d38… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Continue dependency resolver API routes and start work on displaying dependency status on a per repository view Commit: 672480fb1b6e1ff2b58f9f1e1fd11f4692884d74 https://github.com/galaxyproject/galaxy/commit/672480fb1b6e1ff2b58f9f1e1fd1… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Add first pass for displaying dependency status info Commit: a8068679dae232a2eb7f119f367b2c7c7ff76b71 https://github.com/galaxyproject/galaxy/commit/a8068679dae232a2eb7f119f367b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Add name and version to returned dependency Commit: 2a7f67b8b508536ca6828d78f1f3a1c7bfb0460b https://github.com/galaxyproject/galaxy/commit/2a7f67b8b508536ca6828d78f1f3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Hack in name and version into dictified representation of Dependency instance (For NullDependency we do want to show the missing requirements) Commit: 4bd0013648c589deb1be6191ece977dd6e13075c https://github.com/galaxyproject/galaxy/commit/4bd0013648c589deb1be6191ece9… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- add status field with icons Commit: ee33ad8f6065ac9e8c674db61ac939a66eb7c063 https://github.com/galaxyproject/galaxy/commit/ee33ad8f6065ac9e8c674db61ac9… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- whitespace fix Commit: e7f8a13ecb9189c0b1a553bf3532b7849f5cc84e https://github.com/galaxyproject/galaxy/commit/e7f8a13ecb9189c0b1a553bf3532… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Address @nsoranzo's review. - Skip unncessary list() - Sort keys when dumping requirements to json - Rename tools_requirements to all_tools_requirements - Use list comprehension where appropriate Commit: cc085cb9a2f3afb2467e5bbe8192bf6b7a9021bf https://github.com/galaxyproject/galaxy/commit/cc085cb9a2f3afb2467e5bbe8192… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Work on conda install revision Commit: 69480a6c041973d6aa507ba6d2e568f848a7d397 https://github.com/galaxyproject/galaxy/commit/69480a6c041973d6aa507ba6d2e5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Fix dependency typo Commit: 7a8265b0b0f2301516bde01e5b4f7e2bab75baa5 https://github.com/galaxyproject/galaxy/commit/7a8265b0b0f2301516bde01e5b4f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/manage_repository.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Make api return more detailed requirements status, move tool_requirements and tool_requirements_status to Tool class Commit: 983f4a09195be21dcb77fc355b16310ca5e976af https://github.com/galaxyproject/galaxy/commit/983f4a09195be21dcb77fc355b16… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Use list comprehension to generate list of all requirements Commit: 2e7099c772e25c0e0a40c4729716b66c6c132a51 https://github.com/galaxyproject/galaxy/commit/2e7099c772e25c0e0a40c4729716… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix logic error in message Commit: 93579a6373712b53678f585a1a4d074d75d18bdd https://github.com/galaxyproject/galaxy/commit/93579a6373712b53678f585a1a4d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/views.py M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Display whether dependency is exactly resolved (check), inexactly resolved (warning) or not resolved (error) Commit: 602ced89ce31e1d6e6a358f2cfacbe148890b57e https://github.com/galaxyproject/galaxy/commit/602ced89ce31e1d6e6a358f2cfac… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Close docstring example list Commit: f75a28e87c5453b8ed3cc3d2c56d74f5aae37a11 https://github.com/galaxyproject/galaxy/commit/f75a28e87c5453b8ed3cc3d2c56d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Trigger requirement install for new install method Commit: 414bc87d371b3ca593cffaf1b9c49ccb7ade58cd https://github.com/galaxyproject/galaxy/commit/414bc87d371b3ca593cffaf1b9c4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/views.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- flake8 fixes Commit: 4eadf05ae9f9593694d71ecd91e1639c3d24b08a https://github.com/galaxyproject/galaxy/commit/4eadf05ae9f9593694d71ecd91e1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add API endpoint to install (resolver) dependencies Commit: 503915fbdc9707a64fed8849ed77fefa3a0af434 https://github.com/galaxyproject/galaxy/commit/503915fbdc9707a64fed8849ed77… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Correct module description Commit: db0531315823e656662a6ca7d9bcaba7fc7be255 https://github.com/galaxyproject/galaxy/commit/db0531315823e656662a6ca7d9bc… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Trigger dependency installation in InstallRepositoryManager Commit: dcba01846d36de1a19df04203a6d074398cd0388 https://github.com/galaxyproject/galaxy/commit/dcba01846d36de1a19df04203a6d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Add docstring to install_dependency Commit: a8670a2fb096beea324ba86ae5ebf184f4c8854b https://github.com/galaxyproject/galaxy/commit/a8670a2fb096beea324ba86ae5eb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Revert manual_install mode (unncessary, better to use install_dependency) Commit: 6901cb1e9e6a4b3ab67709231251ddfce108809c https://github.com/galaxyproject/galaxy/commit/6901cb1e9e6a4b3ab67709231251… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Introduce installable_resolver property Commit: 33b83e5c70d356168648b022d9c8d106d7182c1b https://github.com/galaxyproject/galaxy/commit/33b83e5c70d356168648b022d9c8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Add install resolver dependency button and add install_resolver_dependency to ToolShedRepositoriesController Commit: 4ed151a771e0f855571c837b604eea1f3baf01fc https://github.com/galaxyproject/galaxy/commit/4ed151a771e0f855571c837b604e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/export_repository.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Revert mako hack to always display install_tool_dependency button - Add resolver checkbox - Add possibility to disable resolvers if initialization failed Commit: 886d074a9ed8c8916a4d29c8397e71df8ac2e0e7 https://github.com/galaxyproject/galaxy/commit/886d074a9ed8c8916a4d29c8397e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-23 (Sat, 23 Jul 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Make conda verbose install check configurable Move dependency installation from resolve() to install_dependency(). Commit: 201863200e824c98c8689b1c5fab145247f49d3c https://github.com/galaxyproject/galaxy/commit/201863200e824c98c8689b1c5fab… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-23 (Sat, 23 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Only return requirements of type package (for now) Commit: 0b242833959a5554d60488d6551da78c816020d4 https://github.com/galaxyproject/galaxy/commit/0b242833959a5554d60488d6551d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-23 (Sat, 23 Jul 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Use resolver.find_dep to determine dependency status Commit: b59b797f5036b492e6abee8757d487ad80e174af https://github.com/galaxyproject/galaxy/commit/b59b797f5036b492e6abee8757d4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Update INDETERMINATE_DEPENDENCY use to NullDependency instance Commit: c10d1cb172eb6458e8ad3ee6ca7f4f27665e619c https://github.com/galaxyproject/galaxy/commit/c10d1cb172eb6458e8ad3ee6ca7f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove unused DependencyResolver view from ToolBox Commit: 49dee6af10fdc81fec37fd593c4bd5537511ccd3 https://github.com/galaxyproject/galaxy/commit/49dee6af10fdc81fec37fd593c4b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Flake8 fix Commit: 6b135c6b1e04726c9cd8644a43601efe1e1cc96c https://github.com/galaxyproject/galaxy/commit/6b135c6b1e04726c9cd8644a4360… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Drop INDETERMINATE_DEPENDENCY alias Commit: dd8f8f1de0adcfec7c85e70e8e60645f664ae697 https://github.com/galaxyproject/galaxy/commit/dd8f8f1de0adcfec7c85e70e8e60… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Fix NullDependency use and add default arguments to NullDependency Commit: b5fad4a04804e6cefec335fe888bf616c7eb7e0d https://github.com/galaxyproject/galaxy/commit/b5fad4a04804e6cefec335fe888b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: A test/integration/test_resolvers.py Log Message: ----------- Add api test for conda dependency resolution Commit: deef480cadaf6161e1f59033925936d7eb7353c1 https://github.com/galaxyproject/galaxy/commit/deef480cadaf6161e1f590339259… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Add more API tests for resolver dependencies Commit: e53a81c40d29686d00580349bae4482f21024a01 https://github.com/galaxyproject/galaxy/commit/e53a81c40d29686d00580349bae4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M test/integration/test_resolvers.py Log Message: ----------- Fix syntax, return None if dependency not found Commit: 9917512f8f2e3193dba0fded5f9927ecb1158095 https://github.com/galaxyproject/galaxy/commit/9917512f8f2e3193dba0fded5f99… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Revert svgwrite import, fixed in #2656 Commit: 645a89170604089c3a0b9e34bd4c50733b2bf3c6 https://github.com/galaxyproject/galaxy/commit/645a89170604089c3a0b9e34bd4c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Remove reference to /tmp Commit: 06e409ad401e4e0d099493e9443886d25a701935 https://github.com/galaxyproject/galaxy/commit/06e409ad401e4e0d099493e94438… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Use continue instead of unused NullDependency in Dependency_Manager.find_dep(), and requirement.version instead of None in Dependency_Manager.find_dep.dependency_shell_commands(). (thanks @nsoranzo) Commit: 2a5b043aaf8da9051ef959e4f9cf2dac99b9383a https://github.com/galaxyproject/galaxy/commit/2a5b043aaf8da9051ef959e4f9cf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Simplify conda install logic Commit: 8cca7bef760691eedadac3e9f377efc22c63f92c https://github.com/galaxyproject/galaxy/commit/8cca7bef760691eedadac3e9f377… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Show conda install option even when no tool_dependencies.xml is available. Also reword different install options, I hope this is more clear - I do think it exposes les of the internal language to the end user. Commit: 483b66be270314859370f1ee84afbdae34460391 https://github.com/galaxyproject/galaxy/commit/483b66be270314859370f1ee84af… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Address @nsoranzo's review Commit: 924a913630f395e26b662171a5075090470b2388 https://github.com/galaxyproject/galaxy/commit/924a913630f395e26b662171a507… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- Mark conda install beta and move after TS options. Commit: 88fac719de191cad6896edb8ac6fcd3058a1accb https://github.com/galaxyproject/galaxy/commit/88fac719de191cad6896edb8ac6f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py Log Message: ----------- Merge remote-tracking branch 'bxlab/install_via_conda' into install_via_conda Commit: 12209ab634634eb8c8a566512dc43b0d9ba78255 https://github.com/galaxyproject/galaxy/commit/12209ab634634eb8c8a566512dc4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Merge pull request #56 from jmchilton/install_via_conda UI Tweaks Commit: a731ce2e22254d086452fc84eca15e65b444762d https://github.com/galaxyproject/galaxy/commit/a731ce2e22254d086452fc84eca1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py A lib/galaxy/tools/toolbox/requirements.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/export_repository.mako A test/integration/test_resolvers.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #2554 from bxlab/install_via_conda Fix bugs in post. Compare: https://github.com/galaxyproject/galaxy/compare/64f4d2192745...a731ce2e2225

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[galaxyproject/galaxy] 6d22f1: Add missing comma to workflow form code
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d22f16a2ed75a03684e34b06e5393790dda9fdd https://github.com/galaxyproject/galaxy/commit/6d22f16a2ed75a03684e34b06e53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Add missing comma to workflow form code Commit: 64f4d2192745f823f0c9d2021c6b543f14fa66cc https://github.com/galaxyproject/galaxy/commit/64f4d2192745f823f0c9d2021c6b… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Merge pull request #2674 from guerler/fix_punctation Add missing comma to workflow form code Compare: https://github.com/galaxyproject/galaxy/compare/e625eed9c575...64f4d2192745

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[galaxyproject/galaxy] 2ecc26: remove unused config; clarify sample; provide defa...
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ecc26d83a517ac7e7452a50d84e9b96e1a9e8af https://github.com/galaxyproject/galaxy/commit/2ecc26d83a517ac7e7452a50d84e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/config.py M templates/base/base_panels.mako Log Message: ----------- remove unused config; clarify sample; provide default for inactive message Commit: c223ebff6dff348acfe70d329657fc71fef605d1 https://github.com/galaxyproject/galaxy/commit/c223ebff6dff348acfe70d329657… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- explicitly disable activation for TS because inherited user controller wants the property Commit: e625eed9c57502996b3f5caa83060bdf001bcada https://github.com/galaxyproject/galaxy/commit/e625eed9c57502996b3f5caa8306… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/config.py M templates/base/base_panels.mako Log Message: ----------- Merge pull request #2158 from martenson/improve-activation activation config touch Compare: https://github.com/galaxyproject/galaxy/compare/3440334694cf...e625eed9c575

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[galaxyproject/galaxy] 04b7d1: Add hg38 to main for ucsc_build_sites.txt.sample
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 04b7d11f053e66b14232440e6ff534a62ff26666 https://github.com/galaxyproject/galaxy/commit/04b7d11f053e66b14232440e6ff5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Add hg38 to main for ucsc_build_sites.txt.sample Commit: 3440334694cfac5967009a45d945b97a06648f9e https://github.com/galaxyproject/galaxy/commit/3440334694cfac5967009a45d945… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #2670 from blankenberg/ucsc-hg38-display Add hg38 to main for ucsc_build_sites.txt.sample Compare: https://github.com/galaxyproject/galaxy/compare/59af87700ddc...3440334694cf

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[galaxyproject/galaxy] a9809c: Use default job history on build_for_rerun unless ...
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a9809ca6925a450115a99e6dafb6f415c95357ad https://github.com/galaxyproject/galaxy/commit/a9809ca6925a450115a99e6dafb6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use default job history on build_for_rerun unless specified otherwise Commit: 59af87700ddca4a6162d2ed55b148196867a9231 https://github.com/galaxyproject/galaxy/commit/59af87700ddca4a6162d2ed55b14… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #2668 from guerler/default_job_history Use default job history on build_for_rerun if current history is unavailable Compare: https://github.com/galaxyproject/galaxy/compare/d9e52c671f80...59af87700ddc

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[galaxyproject/galaxy] a25278: Change default refresh mode for form views
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a25278db670891de06c5159182b0838d47900050 https://github.com/galaxyproject/galaxy/commit/a25278db670891de06c5159182b0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form.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/form/form-view.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Change default refresh mode for form views Commit: d9e52c671f803fd6b320fd2f1cf49d2c00570aa5 https://github.com/galaxyproject/galaxy/commit/d9e52c671f803fd6b320fd2f1cf4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form.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/form/form-view.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #2667 from guerler/add_form_refresh Change default refresh mode for form views Compare: https://github.com/galaxyproject/galaxy/compare/28e7f866cbab...d9e52c671f80

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