- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 47361f: Reduce code duplication by reusing get_installed_r...
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 47361f12ecaad83d5d563be763320ae1b17edc3b https://github.com/galaxyproject/galaxy/commit/47361f12ecaad83d5d563be76332… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce code duplication by reusing get_installed_repository() function. Conflicts: lib/galaxy/tools/toolbox/base.py Commit: e8e01bdfb19cf1cc8f8cf485762c68d3f8e2f352 https://github.com/galaxyproject/galaxy/commit/e8e01bdfb19cf1cc8f8cf485762c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- When loading a tool from Tool Shed, check that the <installed_changeset_revision> element matches the tool path. Workaround for issue #1283, which causes the loaded tool to have a StockLineage instead of a ToolShedLineage, thus creating multiple entries for the tool in the panel. Conflicts: lib/galaxy/tools/toolbox/base.py Commit: bb8f0f75efb971471fa65c2cc6951bfaa00b0fd0 https://github.com/galaxyproject/galaxy/commit/bb8f0f75efb971471fa65c2cc695… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1455 from jmchilton/release_16.01_merge_1 [16.01] Merge #1314 forward into 16.01. Compare: https://github.com/galaxyproject/galaxy/compare/e36d33ce74ba...bb8f0f75efb9

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[galaxyproject/galaxy] ed992b: A large assortment of escaping fixes to primarily ...
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: ed992b3b28c7f6d9d637e82e88305b665733a50b https://github.com/galaxyproject/galaxy/commit/ed992b3b28c7f6d9d637e82e8830… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 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/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/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/mvc/history/multi-panel.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.js 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/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 Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). Commit: 90bed00ebe8a5b4a7e0aeb61c23c991daae03fb8 https://github.com/galaxyproject/galaxy/commit/90bed00ebe8a5b4a7e0aeb61c23c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge 15.07 into 15.10. Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 Conflicts: client/galaxy/scripts/mvc/history/multi-panel.js lib/galaxy/webapps/galaxy/controllers/external_service.py lib/galaxy/webapps/galaxy/controllers/forms.py lib/galaxy/webapps/galaxy/controllers/library_admin.py lib/galaxy/webapps/galaxy/controllers/request_type.py lib/galaxy/webapps/galaxy/controllers/requests_admin.py lib/galaxy/webapps/galaxy/controllers/requests_common.py lib/galaxy/webapps/galaxy/controllers/visualization.py lib/galaxy/webapps/reports/controllers/jobs.py lib/galaxy/webapps/reports/controllers/sample_tracking.py lib/galaxy/webapps/reports/controllers/workflows.py lib/tool_shed/grids/admin_grids.py lib/tool_shed/grids/repository_grids.py lib/tool_shed/grids/repository_review_grids.py static/maps/mvc/history/multi-panel.js.map static/maps/mvc/ui/ui-select-default.js.map static/scripts/mvc/collection/list-collection-creator.js static/scripts/mvc/collection/list-of-pairs-collection-creator.js static/scripts/mvc/dataset/dataset-li-edit.js static/scripts/mvc/dataset/dataset-li.js static/scripts/mvc/history/history-panel.js static/scripts/mvc/history/multi-panel.js static/scripts/mvc/list/list-panel.js static/scripts/mvc/ui/ui-select-default.js Commit: c13b1c088cfbb0c708b2ce1d9068c704aba6cc95 https://github.com/galaxyproject/galaxy/commit/c13b1c088cfbb0c708b2ce1d9068… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge pull request #1458 from jmchilton/release_15.10_merge_0 [15.10] Merge 15.07 into 15.10. Compare: https://github.com/galaxyproject/galaxy/compare/7b45f7b40473...c13b1c088cfb

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[galaxyproject/galaxy] cd1cc9: Implement code from @natefoo comment
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd1cc96d5d565299168ac03371d664789bba783b https://github.com/galaxyproject/galaxy/commit/cd1cc96d5d565299168ac03371d6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M Makefile Log Message: ----------- Implement code from @natefoo comment https://github.com/galaxyproject/galaxy/issues/715#issuecomment-169148056 Commit: d848f83e8d0a49f108659838165dffaeeb2939cd https://github.com/galaxyproject/galaxy/commit/d848f83e8d0a49f108659838165d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M Makefile Log Message: ----------- Correct name, minor version Commit: f8072a8e486c4d3d36d946246faf647e3495a5c7 https://github.com/galaxyproject/galaxy/commit/f8072a8e486c4d3d36d946246faf… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M Makefile Log Message: ----------- Configurable upstream Commit: 35c80067ab690bed89457c18ecc14fc5053a8dea https://github.com/galaxyproject/galaxy/commit/35c80067ab690bed89457c18ecc1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #1433 from erasche/release-process Add makefile target for release process Compare: https://github.com/galaxyproject/galaxy/compare/ca40d376f7e5...35c80067ab69

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[galaxyproject/galaxy] a964fc: Add run_toolshed_tests.html to .gitignore .
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a964fcc204eeebfaa5c193a8833e399b4abccee9 https://github.com/galaxyproject/galaxy/commit/a964fcc204eeebfaa5c193a8833e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M .gitignore Log Message: ----------- Add run_toolshed_tests.html to .gitignore . Commit: ca40d376f7e589f02605bb622444e7e3dd6ba934 https://github.com/galaxyproject/galaxy/commit/ca40d376f7e589f02605bb622444… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M .gitignore Log Message: ----------- Merge pull request #1456 from nsoranzo/gitignore Add run_toolshed_tests.html to .gitignore . Compare: https://github.com/galaxyproject/galaxy/compare/89781f74a593...ca40d376f7e5

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[galaxyproject/galaxy] 9b4ff6: Clean up: remove print statements in templates
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b4ff63a16edb651ada88a579dc4fbe839e7c85c https://github.com/galaxyproject/galaxy/commit/9b4ff63a16edb651ada88a579dc4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M templates/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Clean up: remove print statements in templates Commit: 89781f74a593943e7d1271a9a68ab0a770ef2bf6 https://github.com/galaxyproject/galaxy/commit/89781f74a593943e7d1271a9a68a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M templates/grid_base.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- Merge pull request #1454 from carlfeberhard/cleanup.grid_template Clean up: remove print statements in templates Compare: https://github.com/galaxyproject/galaxy/compare/7f81a8def003...89781f74a593

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[galaxyproject/galaxy] 07d574: Fix that typo.
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07d574c510611044a1f6bdba1de173ec1a0ad662 https://github.com/galaxyproject/galaxy/commit/07d574c510611044a1f6bdba1de1… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/tool_shed/dependencies/repository/relation_builder.py Log Message: ----------- Fix that typo. Commit: 7f81a8def003f46ba08c9a00b794674c371dc79b https://github.com/galaxyproject/galaxy/commit/7f81a8def003f46ba08c9a00b794… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/tool_shed/dependencies/repository/relation_builder.py Log Message: ----------- Merge pull request #1453 from davebx/that_typo Fix that typo in relation_builder. Compare: https://github.com/galaxyproject/galaxy/compare/33d533812920...7f81a8def003

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[galaxyproject/galaxy] d05ee5: Empty cherry-pick of 93c6d05 to cleanup merge.
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: d05ee507253901ef69a8892f6820b953c8d05725 https://github.com/galaxyproject/galaxy/commit/d05ee507253901ef69a8892f6820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Empty cherry-pick of 93c6d05 to cleanup merge. Commit: e36d33ce74babd939b3e70f30f0bf84f3cd2e527 https://github.com/galaxyproject/galaxy/commit/e36d33ce74babd939b3e70f30f0b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Log Message: ----------- Merge pull request #1451 from jmchilton/release_16.01_merge_0 [16.01] Empty cherry-pick of 93c6d05 to cleanup merge 15.10 -> 16.01 Compare: https://github.com/galaxyproject/galaxy/compare/88a1e636b8de...e36d33ce74ba

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[galaxyproject/galaxy] 7a3cc4: Fix optional watchdog handling.
by GitHub 08 Jan '16

08 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 7a3cc410549474de18ff195c0e1dcd76fa92f64b https://github.com/galaxyproject/galaxy/commit/7a3cc410549474de18ff195c0e1d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Fix optional watchdog handling. Broken with 4086dd61dafe562ec01a8b1fce687a539aedbcfe. Thanks for bug report from @nsoranzo. Commit: e611b8fdb80beb87196a685924abe8e71bedcbea https://github.com/galaxyproject/galaxy/commit/e611b8fdb80beb87196a685924ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Use a more typical optional default value for optional import in watcher.py. Thanks to @nsoranzo for the advice - https://github.com/galaxyproject/galaxy/pull/1448#discussion_r49210125. Commit: 88a1e636b8dea04a0db7d557fa6eb1483097b69d https://github.com/galaxyproject/galaxy/commit/88a1e636b8dea04a0db7d557fa6e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-08 (Fri, 08 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #1448 from jmchilton/watcher_fix [16.01] Fix optional watchdog handling. Compare: https://github.com/galaxyproject/galaxy/compare/5d32c9f8fc7e...88a1e636b8de

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[galaxyproject/galaxy] 2f760a: Fix formatting.
by GitHub 06 Jan '16

06 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2f760a2e6d3cc098e144a24931cf0af2369e2f44 https://github.com/galaxyproject/galaxy/commit/2f760a2e6d3cc098e144a24931cf… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Fix formatting. Commit: 33d533812920c1bc0e5998cd5564f5da716fc237 https://github.com/galaxyproject/galaxy/commit/33d533812920c1bc0e5998cd5564… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-06 (Wed, 06 Jan 2016) Changed paths: M doc/source/project/issues.rst Log Message: ----------- Merge pull request #1440 from davebx/proc_formatting Fix formatting in issues.rst Compare: https://github.com/galaxyproject/galaxy/compare/3b4fd544cecf...33d533812920

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[galaxyproject/galaxy] 073609: Fix casper tests.
by GitHub 06 Jan '16

06 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 05 Jan '16

05 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 05 Jan '16

05 Jan '16

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

1 0

[galaxyproject/galaxy]
by GitHub 05 Jan '16

05 Jan '16

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

1 0

[galaxyproject/galaxy]
by GitHub 05 Jan '16

05 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 05 Jan '16

05 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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[galaxyproject/galaxy] 1568c0: fix title_default to work as a default and not an ...
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1568c0db809988599f10aebe1a24457087a49a1d https://github.com/galaxyproject/galaxy/commit/1568c0db809988599f10aebe1a24… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- fix title_default to work as a default and not an override Commit: 0ae86f59a1f491eaa022676cdac76fce251eb322 https://github.com/galaxyproject/galaxy/commit/0ae86f59a1f491eaa022676cdac7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Merge pull request #1429 from dannon/interactive_tours fix title_default to work as a default and not an override Compare: https://github.com/galaxyproject/galaxy/compare/ddc2a12eb18e...0ae86f59a1f4

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[galaxyproject/galaxy] 237ecc: Add form help class
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 237ecc77898f90d8d2d5d95741ff6fbaecc9e936 https://github.com/galaxyproject/galaxy/commit/237ecc77898f90d8d2d5d95741ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-template.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-template.js M static/style/blue/base.css Log Message: ----------- Add form help class Commit: ddc2a12eb18e036e2e5cad072eb4ea99328ec7b2 https://github.com/galaxyproject/galaxy/commit/ddc2a12eb18e036e2e5cad072eb4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/style/less/ui.less M static/maps/mvc/tool/tool-template.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-template.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1428 from guerler/add_pseudo_class_000 Add form help class Compare: https://github.com/galaxyproject/galaxy/compare/8bd293683bd2...ddc2a12eb18e

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[galaxyproject/galaxy] c41642: Remove dup NiceConfigParser from loadwsgi.py.
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c416426522c7cf8f684f12937a42354abd4ce875 https://github.com/galaxyproject/galaxy/commit/c416426522c7cf8f684f12937a42… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py Log Message: ----------- Remove dup NiceConfigParser from loadwsgi.py. We are really adopting pastescript as our own. Commit: 39f5c5d207f091f214b87d391a5aefb47402b9fc https://github.com/galaxyproject/galaxy/commit/39f5c5d207f091f214b87d391a5a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make docutils an optional dependency of galaxy-lib. Commit: 951b95e07964885e2fac88b685f498aca2f3e7fc https://github.com/galaxyproject/galaxy/commit/951b95e07964885e2fac88b685f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/multi_byte.py Log Message: ----------- Make wchartype an optional dependency of galaxy-lib. Commit: 8bd293683bd2144a877ec7206c003d52892c5796 https://github.com/galaxyproject/galaxy/commit/8bd293683bd2144a877ec7206c00… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/multi_byte.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py Log Message: ----------- Merge pull request #1427 from jmchilton/lib-deps Revise galaxy-lib dependencies. Compare: https://github.com/galaxyproject/galaxy/compare/0bad80ebdf2a...8bd293683bd2

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[galaxyproject/galaxy] 2be9aa: cram datatype: support for crai indexes via pysam
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2be9aa2569b35a86f4c593215189a07eb5dd62f0 https://github.com/galaxyproject/galaxy/commit/2be9aa2569b35a86f4c593215189… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- cram datatype: support for crai indexes via pysam Commit: d7eb84e57bbd119d788ca759e0d61a464a030c7a https://github.com/galaxyproject/galaxy/commit/d7eb84e57bbd119d788ca759e0d6… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- cram datatype: support for crai index (using built-in pysam) Commit: 78558beec3ebeca63a282e667948a18c2b21c508 https://github.com/galaxyproject/galaxy/commit/78558beec3ebeca63a282e667948… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- cram datatype definition: flake8 correction Commit: 0bad80ebdf2a36ae23e05b1dee6152ee387b3b79 https://github.com/galaxyproject/galaxy/commit/0bad80ebdf2a36ae23e05b1dee61… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #1182 from yhoogstrate/bam_cram_index_via_pysam cram datatype: crai index via pysam Compare: https://github.com/galaxyproject/galaxy/compare/634a5b7fd9f2...0bad80ebdf2a

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[galaxyproject/galaxy] ce2795: Copy pastescript's NiceConfigParser into galaxy.ut...
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce2795d87ca4e5063ca699ad75cb6e4461fba30c https://github.com/galaxyproject/galaxy/commit/ce2795d87ca4e5063ca699ad75cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-03 (Sun, 03 Jan 2016) Changed paths: M lib/galaxy/util/properties.py Log Message: ----------- Copy pastescript's NiceConfigParser into galaxy.util.properties. This is used in galaxy-lib and by utilities such as galaxy/main.py which has no reason to depend on pastescript. Commit: 634a5b7fd9f289c09a963f19a9db36937fc301c9 https://github.com/galaxyproject/galaxy/commit/634a5b7fd9f289c09a963f19a9db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/util/properties.py Log Message: ----------- Merge pull request #1413 from jmchilton/lib_0 Copy pastescript's NiceConfigParser into galaxy.util.properties. Compare: https://github.com/galaxyproject/galaxy/compare/6bd854ebe428...634a5b7fd9f2

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[galaxyproject/galaxy] 0203a6: Tours.
by GitHub 05 Jan '16

05 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0203a69d88c854c1fe3a210c83ff3ee0d943f4df https://github.com/galaxyproject/galaxy/commit/0203a69d88c854c1fe3a210c83ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/grunt-tasks/install-libs.js M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/tours/__init__.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map A static/maps/libs/bootstrap-tour.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/upload/upload-button.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/menu.js A static/scripts/libs/bootstrap-tour.js A static/scripts/mvc/tours.js M static/scripts/mvc/upload/upload-button.js M static/style/blue/base.css A static/style/blue/bootstrap-tour.css M templates/base.mako M templates/base/base_panels.mako Log Message: ----------- Tours. Commit: 40382fb0c1d7ec38252413aa50b3cb24418d158e https://github.com/galaxyproject/galaxy/commit/40382fb0c1d7ec38252413aa50b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: A config/plugins/tours/galaxy_ui.yaml Log Message: ----------- Add slightly modified intro tour from bjoern, mostly compatible. Commit: f107b17928bddbe4f87e757f2301d56b807253cf https://github.com/galaxyproject/galaxy/commit/f107b17928bddbe4f87e757f2301… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js M client/webpack.config.js M static/maps/mvc/tours.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/tours.js Log Message: ----------- Refactor a bit, adjust textinsert action to trigger 'change' on the element. Commit: 1e5640163a36c12e5f9e719358a1653a0fb18401 https://github.com/galaxyproject/galaxy/commit/1e5640163a36c12e5f9e719358a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Tour shim in onload, check sessionStorage (or would local be more appropriate?) Commit: 7110a0cc5e411062b8c6e5857e04ce10f121ffdd https://github.com/galaxyproject/galaxy/commit/7110a0cc5e411062b8c6e5857e04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Document necessary tweak. Commit: 9e7eaaa7aaf9c9a6928edc08abecbc26a3a76004 https://github.com/galaxyproject/galaxy/commit/9e7eaaa7aaf9c9a6928edc08abec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Finish sessionStorage and restart of tours across multiple pages. Commit: 5a3524245b41f2978b81ee01176dcf1caa382d50 https://github.com/galaxyproject/galaxy/commit/5a3524245b41f2978b81ee01176d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Actually let people end a tour. Commit: ffede653023a49aabcfcc958816b20e0e183a4ba https://github.com/galaxyproject/galaxy/commit/ffede653023a49aabcfcc958816b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Debugging cruft. Commit: 8c1beb2af5633660efc8ec7caaa871416f2508ea https://github.com/galaxyproject/galaxy/commit/8c1beb2af5633660efc8ec7caaa8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- title override, working on fixing style. Commit: 4efa8e73b3479f3914b6b54d6a8bc4651aec7ef4 https://github.com/galaxyproject/galaxy/commit/4efa8e73b3479f3914b6b54d6a8b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Consolidate to standard options dict, minor refactorings. Commit: 38b3c6e97aa0d6fe595be0f6e9021109ddd17226 https://github.com/galaxyproject/galaxy/commit/38b3c6e97aa0d6fe595be0f6e902… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Build client, bundle. Commit: 9b14d515db16d3a769532740a9b807b37a1177bd https://github.com/galaxyproject/galaxy/commit/9b14d515db16d3a769532740a9b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M static/style/blue/bootstrap-tour.css M templates/base/base_panels.mako M templates/js-app.mako Log Message: ----------- Stylize! Commit: e8116b8bbf22373ae8e784e83cf55426fd5b60bc https://github.com/galaxyproject/galaxy/commit/e8116b8bbf22373ae8e784e83cf5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less M static/style/blue/base.css Log Message: ----------- Flip global vars back, now that bootstrap-tours.css is included and will override. Commit: aecc5d864f8e211c6f60ea8717f726c5807a1a76 https://github.com/galaxyproject/galaxy/commit/aecc5d864f8e211c6f60ea8717f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/tours/galaxy_ui.yaml M static/maps/mvc/tours.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Make tours.js safe (but possibly not functional wrt/ listing) to use on pages without Galaxy object. Commit: 2c5241dc3bba2114b43fe7f7e6e2efb17b705a28 https://github.com/galaxyproject/galaxy/commit/2c5241dc3bba2114b43fe7f7e6e2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Full client rebuild. Commit: e325eba37c159e78a20895edbd6d521657f9b650 https://github.com/galaxyproject/galaxy/commit/e325eba37c159e78a20895edbd6d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py M lib/galaxy/webapps/galaxy/api/tours.py M static/maps/mvc/tours.js.map 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/tours.js Log Message: ----------- Some tweaks care of @bgruening. This adds (slightly tweaked) functionality to support a series of clicks, still needs a delay between clicks, and since it's the most common case that pre/postclick will be a single item, a list shouldn't be required here. Commit: 578e201d64aa33224a586fe7928a8be5b476d332 https://github.com/galaxyproject/galaxy/commit/578e201d64aa33224a586fe7928a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-28 (Mon, 28 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map 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/tours.js M static/scripts/onload.js Log Message: ----------- Launch tour on GET arg (?tour_id=core.galaxy_ui). Commit: 4322f5e9b9e152aec75339925228b90ef759b47b https://github.com/galaxyproject/galaxy/commit/4322f5e9b9e152aec75339925228… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-29 (Tue, 29 Dec 2015) Changed paths: A config/plugins/tours/core.galaxy_ui.yaml R config/plugins/tours/galaxy_ui.yaml M lib/galaxy/tours/__init__.py Log Message: ----------- Force tour_id to be locked to filename, instead of allowing these to be out of sync. Commit: 401583d730a6d5d1e57c82bb08c3216b40856d8f https://github.com/galaxyproject/galaxy/commit/401583d730a6d5d1e57c82bb08c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-29 (Tue, 29 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Move TOURS.giveTour at the top level of the namespace instead of a method of the view. Commit: 603cb2f18dfc1f4518066e514f660f7db91eb45d https://github.com/galaxyproject/galaxy/commit/603cb2f18dfc1f4518066e514f66… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: A config/plugins/tours/core.history.yaml Log Message: ----------- Add history tour from @bgruening Commit: d23541092070b3dff9ef18a56620fc93837d9233 https://github.com/galaxyproject/galaxy/commit/d23541092070b3dff9ef18a56620… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Remove tour id from tour; unique and namespaced by filename and not a separate identifier. Commit: e243fe3bc1e66dfcb9de778e66ff99028c56f358 https://github.com/galaxyproject/galaxy/commit/e243fe3bc1e66dfcb9de778e66ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Slight refactoring, fix .yaml stripping bug. Commit: 0ef88e1e5397bc094a4a0f9f9683fdaffab35f48 https://github.com/galaxyproject/galaxy/commit/0ef88e1e5397bc094a4a0f9f9683… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add tour reloading API endpoint. Commit: b9faf84b245a39780373545f778586bcc9ace916 https://github.com/galaxyproject/galaxy/commit/b9faf84b245a39780373545f7785… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: A test/api/test_tours.py Log Message: ----------- Stub an API test for tours so I can refactor a little. Commit: 01fed4b6d4d473d81fe2e89ee8199b00d0815a00 https://github.com/galaxyproject/galaxy/commit/01fed4b6d4d473d81fe2e89ee819… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tours/__init__.py Log Message: ----------- Allow .yml extensions. Though not the "official" extension for YAML files, it is actually seen much more common in the wild. Commit: b35a39bd55d088fa25d2b3999fa482b83055f38a https://github.com/galaxyproject/galaxy/commit/b35a39bd55d088fa25d2b3999fa4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tours.py Log Message: ----------- Prefer self.app to trans.app. See comments here https://github.com/galaxyproject/galaxy/pull/1392#commitcomment-15141262 for instance for argument why this is superior. Commit: da8b943f538d55c2d8290870eb19210c831cb627 https://github.com/galaxyproject/galaxy/commit/da8b943f538d55c2d8290870eb19… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: 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 M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.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-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.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 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 M config/plugins/visualizations/charts/templates/charts.mako M config/tool_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/binary.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/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/tools/__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/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/basic.py M lib/galaxy/tools/parameters/history_query.py A lib/galaxy/tools/parameters/wrapped_json.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.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/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 M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/directory_hash.py M lib/galaxy/util/expressions.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/topsort.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.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 M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.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/common_util.py M lib/tool_shed/util/tool_util.py M run.sh M run_tests.sh M scripts/common_startup.sh 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 M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.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-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/workflow/workflow-terminals.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 M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.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-ftp.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/onload.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M static/style/blue/masthead.css M templates/admin/reload_tool.mako M templates/webapps/galaxy/galaxy.masthead.mako A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.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_objectstore.py M test/unit/test_routes.py A test/unit/tools/test_conda_resolution.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 tox.ini Log Message: ----------- Merge. Commit: 7587809bb6f08a1ff4754b8d13b8ebfafaabc259 https://github.com/galaxyproject/galaxy/commit/7587809bb6f08a1ff4754b8d13b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py Log Message: ----------- Improve tour directory logic. - Refactor plugin framework logic for finding configuration directories out into util. - Rework tours to use the plugin framework logic to parse configuration directories. - Rework tour logic to allow multiple tour configuration directories. - Fix up config.ini.sample comments on interactive environments and tours to reflect these changes and include more information like the viz directory does. Commit: c28d4d01eef483a2c8255f1ac14d636ab60351a7 https://github.com/galaxyproject/galaxy/commit/c28d4d01eef483a2c8255f1ac14d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Correctly specify default tour location. Commit: 4ef3e21c954a8bfe5b12758252ffcb5b303445f8 https://github.com/galaxyproject/galaxy/commit/4ef3e21c954a8bfe5b12758252ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Fix onclick handling broken w/ #1407 Commit: 5c765c08715c17c07c1916c8c7a484d8ef71a954 https://github.com/galaxyproject/galaxy/commit/5c765c08715c17c07c1916c8c7a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'dev' into interactive_tours Commit: 1d97e4271ef40969bb117e424691418ccecec7a2 https://github.com/galaxyproject/galaxy/commit/1d97e4271ef40969bb117e424691… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge dev to include menu/onclick fix. Commit: 1876ea6bb2565ccaf7f6475f9387e43f91e34bb5 https://github.com/galaxyproject/galaxy/commit/1876ea6bb2565ccaf7f6475f9387… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/tours.py A test/api/test_tours.py Log Message: ----------- Merge pull request #8 from jmchilton/interactive_tours Minor tweaks to interactive tours backend. Commit: 5924857c2c7e012875b9840811ab22b9d4935cfa https://github.com/galaxyproject/galaxy/commit/5924857c2c7e012875b9840811ab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js Log Message: ----------- Fix pre/postclick that got broken somewhere along the way w/ patches&merges. Commit: 9416e6f3f75513f8e86f741d5c2f322708abdb0b https://github.com/galaxyproject/galaxy/commit/9416e6f3f75513f8e86f741d5c2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-frames.js Log Message: ----------- Merge and resolve conflicts, rebuilding. Commit: 3d1b3f9806007e456ea5f409df5be96b69aabdb7 https://github.com/galaxyproject/galaxy/commit/3d1b3f9806007e456ea5f409df5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- How'd that get there? Commit: a1a549ea67b28679b079f4150cf6ce18bc87dd56 https://github.com/galaxyproject/galaxy/commit/a1a549ea67b28679b079f4150cf6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js Log Message: ----------- Re-add identifiers to masthead, new ones for scratchbook (thanks @guerler) Commit: 6bd854ebe428a69f2e5664448330b8a4b2aafe77 https://github.com/galaxyproject/galaxy/commit/6bd854ebe428a69f2e5664448330… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/bower.json M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/onload.js M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/galaxy.ini.sample A config/plugins/tours/core.galaxy_ui.yaml A config/plugins/tours/core.history.yaml M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/pluginframework.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/galaxy.menu.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map A static/maps/libs/bootstrap-tour.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/galaxy.menu.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js A static/scripts/libs/bootstrap-tour.js A static/scripts/mvc/tours.js M static/scripts/mvc/upload/upload-button.js M static/scripts/onload.js A static/style/blue/bootstrap-tour.css M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako A test/api/test_tours.py Log Message: ----------- Merge pull request #1422 from dannon/interactive_tours Interactive Tours Compare: https://github.com/galaxyproject/galaxy/compare/1730c12f8d3b...6bd854ebe428

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