January 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 073609: Fix casper tests.
by GitHub 07 Jan '16

07 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 073609d005d2e5d109e7f55b839058dce005ca95 https://github.com/galaxyproject/galaxy/commit/073609d005d2e5d109e7f55b8390… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Fix casper tests. Commit: 5d32c9f8fc7ef8f287df2a1047dc1c394d9d791d https://github.com/galaxyproject/galaxy/commit/5d32c9f8fc7ef8f287df2a1047dc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Merge pull request #1439 from jmchilton/backport_casper_fixes [16.01] Fix casper tests. Compare: https://github.com/galaxyproject/galaxy/compare/291d7751707d...5d32c9f8fc7e

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[galaxyproject/galaxy] 06fd21: Fix casper tests.
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 06fd219646b6bcb1aa3a5ce54c62cd2b3a804716 https://github.com/galaxyproject/galaxy/commit/06fd219646b6bcb1aa3a5ce54c62… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Fix casper tests. Commit: 2b80dd2da97e3253e238a60d0d1b0a9e6bc57817 https://github.com/galaxyproject/galaxy/commit/2b80dd2da97e3253e238a60d0d1b… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: A .ci/flake8_py3_wrapper.sh A .ci/py3_sources.txt M client/bower.json M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-template.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less R client/galaxy/style/less/masthead.less M client/galaxy/style/less/ui.less M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako A config/plugins/tours/core.galaxy_ui.yaml A config/plugins/tours/core.history.yaml M config/plugins/visualizations/charts/templates/charts.mako M config/tool_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M doc/source/lib/galaxy.datatypes.converters.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/checkers.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.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 A lib/galaxy/tools/deps/views.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py A lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/special_tools.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py A lib/galaxy/util/checkers.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/directory_hash.py M lib/galaxy/util/expressions.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/topsort.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M run.sh M run_tests.sh M scripts/common_startup.sh A static/maps/galaxy.menu.js.map M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map A static/maps/libs/bootstrap-tour.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-template.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.js.map M static/maps/utils/uploadbox.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 A static/scripts/galaxy.menu.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js A static/scripts/libs/bootstrap-tour.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-template.js A static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css A static/style/blue/bootstrap-tour.css M static/style/blue/masthead.css M templates/admin/reload_tool.mako M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/workflow/editor.mako A test/api/test_tours.py A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-app.js A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/tools/test_actions.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fix_casper Commit: d844a3489bbfecf3d3a2824e847e99ade6ce707b https://github.com/galaxyproject/galaxy/commit/d844a3489bbfecf3d3a2824e847e… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M test/casperjs/modules/user.js Log Message: ----------- Remove debugs. Commit: 3b4fd544cecf0498917bdd5a5689b436223361a7 https://github.com/galaxyproject/galaxy/commit/3b4fd544cecf0498917bdd5a5689… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M test/casperjs/api-tool-tests.js M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js Log Message: ----------- Merge pull request #1438 from davebx/fix_casper Fix casper tests Compare: https://github.com/galaxyproject/galaxy/compare/2a64f5c9ae10...3b4fd544cecf

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[galaxyproject/galaxy] a0610e: Update version to 16.01.rc1
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0610ecdc0b070a671d4439378e3e9629b8d337e https://github.com/galaxyproject/galaxy/commit/a0610ecdc0b070a671d4439378e3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.01.rc1 Commit: a4b252bd49a1bd2081c82c256d83703128fdb3f6 https://github.com/galaxyproject/galaxy/commit/a4b252bd49a1bd2081c82c256d83… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.04.dev Commit: e9f6a730cbda18f07e12c4c4e16ceff170b7f1fe https://github.com/galaxyproject/galaxy/commit/e9f6a730cbda18f07e12c4c4e16c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Log Message: ----------- Merge branch 'version-16.01' into version-16.04.dev Commit: 2a64f5c9ae102e7fc9a2c7f6c19a20d956f7d2dc https://github.com/galaxyproject/galaxy/commit/2a64f5c9ae102e7fc9a2c7f6c19a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1431 from natefoo/version-16.04.dev Update version to 16.04.dev and handle the resulting merge conflict from release_16.01 Compare: https://github.com/galaxyproject/galaxy/compare/016fd38e72ee...2a64f5c9ae10

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[galaxyproject/galaxy] 243f7a: Added bcf_bgzip to bcf converter
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 243f7a5be29afba188fbd03c7651c6e3cecf02ab https://github.com/galaxyproject/galaxy/commit/243f7a5be29afba188fbd03c7651… Author: Mark Iskander <motiontracker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: A lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.xml Log Message: ----------- Added bcf_bgzip to bcf converter Commit: f800494eebd3238f7d22b4c0d77795d4e65672a2 https://github.com/galaxyproject/galaxy/commit/f800494eebd3238f7d22b4c0d777… Author: Mark Iskander <motiontracker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: 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/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/util/xml_macros.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge branch 'dev' into bcfgz_to_bcf_converter Commit: 6cd550e0c7844cf89289f8ff25b9e3995b2d0bac https://github.com/galaxyproject/galaxy/commit/6cd550e0c7844cf89289f8ff25b9… Author: Mark Iskander <motiontracker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M doc/source/lib/galaxy.datatypes.converters.rst A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.xml R lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.py R lib/galaxy/datatypes/converters/bcfgz_to_bcf_converter.xml Log Message: ----------- Added the bcf_bgzip_to_bcf converter to datatype.converters.rst, renamed files to follow standard naming scheme Commit: 39070a33c02b27107dd9eac9419f30d3cde4b489 https://github.com/galaxyproject/galaxy/commit/39070a33c02b27107dd9eac9419f… Author: Mark Iskander <motiontracker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'dev' into bcfgz_to_bcf_converter Commit: 825a20ef8138d04b25ebb5bea907abe23abc889d https://github.com/galaxyproject/galaxy/commit/825a20ef8138d04b25ebb5bea907… Author: Mark Iskander <motiontracker(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M doc/source/lib/galaxy.datatypes.converters.rst R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.py R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf.xml A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml Log Message: ----------- Modified more names, added bcf_bgzip to datatypes, added converters going both ways Commit: 016fd38e72eeb6466c10f36fe5cba9fe6d820775 https://github.com/galaxyproject/galaxy/commit/016fd38e72eeb6466c10f36fe5cb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M config/datatypes_conf.xml.sample M doc/source/lib/galaxy.datatypes.converters.rst A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml Log Message: ----------- Merge pull request #1148 from markiskander/bcfgz_to_bcf_converter Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type Compare: https://github.com/galaxyproject/galaxy/compare/b4fe6e2c3d9b...016fd38e72ee

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[galaxyproject/usegalaxy-playbook] 344689: Temporarly disable the NVC dynamic rule due to an ...
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3446891b3a39703f6e739a164eb679feb36ed4ee https://github.com/galaxyproject/usegalaxy-playbook/commit/3446891b3a39703f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Temporarly disable the NVC dynamic rule due to an exception. Allocate more memory for the HISAT2 DM.

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[galaxyproject/galaxy] a0610e: Update version to 16.01.rc1
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: a0610ecdc0b070a671d4439378e3e9629b8d337e https://github.com/galaxyproject/galaxy/commit/a0610ecdc0b070a671d4439378e3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.01.rc1 Commit: 291d7751707d2382c1d3a24b01fafec4ae757748 https://github.com/galaxyproject/galaxy/commit/291d7751707d2382c1d3a24b01fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1430 from natefoo/version-16.01 [16.01] Update version to 16.01.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/b4fe6e2c3d9b...291d7751707d

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[galaxyproject/galaxy]
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy]
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy]
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 6ca159: Added hashes
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6ca159136638e54a0fe9fe471202aaa788987cf1 https://github.com/galaxyproject/galaxy/commit/6ca159136638e54a0fe9fe471202… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-23 (Wed, 23 Dec 2015) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Added hashes Fixes #1260 Commit: b4fe6e2c3d9b77593f00ef6aa4a2e3611f3125ad https://github.com/galaxyproject/galaxy/commit/b4fe6e2c3d9b77593f00ef6aa4a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #1393 from erasche/requirements-hashes-round-3 Added hashes Compare: https://github.com/galaxyproject/galaxy/compare/0ae86f59a1f4...b4fe6e2c3d9b

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