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

[galaxyproject/usegalaxy-playbook] f1d245: Installed MiModD 0.8.1
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f1d2455635aec3d88c354061f106adb53081465f https://github.com/galaxyproject/usegalaxy-playbook/commit/f1d2455635aec3d8… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed MiModD 0.8.1

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[galaxyproject/usegalaxy-playbook] f01373: Fix BAM metadata issues on Jetstream
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f01373fe9596a3eafec883d7c3bcc76cab433c91 https://github.com/galaxyproject/usegalaxy-playbook/commit/f01373fe9596a3ea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M CHANGELOG.md M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fix BAM metadata issues on Jetstream

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[galaxyproject/galaxy] 0a6c29: Add missing ipaddress requirement
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a6c2974204b3048456bc7ceba7793ab4774de9f https://github.com/galaxyproject/galaxy/commit/0a6c2974204b3048456bc7ceba77… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add missing ipaddress requirement Broken in https://github.com/galaxyproject/galaxy/pull/4289 . Fix https://github.com/galaxyproject/galaxy/issues/4999 . Commit: 18467e9b2cecb2102d17fd6734f1fb40c5321623 https://github.com/galaxyproject/galaxy/commit/18467e9b2cecb2102d17fd6734f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement [17.09] Add missing ipaddress requirement Commit: 7bede53beff349b393c3c5a293902def1d8bdb76 https://github.com/galaxyproject/galaxy/commit/7bede53beff349b393c3c5a29390… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge branch 'release_17.09' into dev Conflicts: lib/galaxy/dependencies/pinned-requirements.txt lib/galaxy/dependencies/requirements.txt Compare: https://github.com/galaxyproject/galaxy/compare/f34e6a1e2e18...7bede53beff3

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[galaxyproject/galaxy] c99400: add askomics interactive environment
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c994005fcc2b06bacfaf992be9de9002c47b5ab3 https://github.com/galaxyproject/galaxy/commit/c994005fcc2b06bacfaf992be9de… Author: xgaia <xgaia(a)gmx.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: A config/plugins/interactive_environments/askomics/LICENSE A config/plugins/interactive_environments/askomics/README.md A config/plugins/interactive_environments/askomics/config/allowed_images.yml A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako Log Message: ----------- add askomics interactive environment Commit: 4d5facb9857e2f7b70282e74f40d0b31d1120d41 https://github.com/galaxyproject/galaxy/commit/4d5facb9857e2f7b70282e74f40d… Author: xgaia <xgaia(a)gmx.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: R config/plugins/interactive_environments/askomics/README.md R config/plugins/interactive_environments/askomics/config/allowed_images.yml Log Message: ----------- remove files Commit: e55121f655ca105f2d9ac7ea473cca77c6f07b75 https://github.com/galaxyproject/galaxy/commit/e55121f655ca105f2d9ac7ea473c… Author: xgaia <xgaia(a)gmx.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: R config/plugins/interactive_environments/askomics/LICENSE Log Message: ----------- remove license file Commit: 04370ebff931ed2f591531f2cf58b8248e71f956 https://github.com/galaxyproject/galaxy/commit/04370ebff931ed2f591531f2cf58… Author: xgaia <xgaia(a)gmx.com> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M config/plugins/interactive_environments/askomics/templates/askomics.mako Log Message: ----------- use build-in password generator for api key Commit: 1d5f0d2b611c3685cc12b95a0efdb91e3e4d872b https://github.com/galaxyproject/galaxy/commit/1d5f0d2b611c3685cc12b95a0efd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M config/plugins/interactive_environments/askomics/static/js/askomics.js M config/plugins/interactive_environments/askomics/templates/askomics.mako Log Message: ----------- Fixes to askomics javascript Commit: 7d674e1de0d23b48d3f6a8cf0fc4c5a2d883d9e7 https://github.com/galaxyproject/galaxy/commit/7d674e1de0d23b48d3f6a8cf0fc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M config/plugins/interactive_environments/askomics/static/js/askomics.js Log Message: ----------- Left off semicolon. Commit: 8d3c8c6d40521ec513b936dd4b15693edf0f280b https://github.com/galaxyproject/galaxy/commit/8d3c8c6d40521ec513b936dd4b15… Author: Xavier Garnier <xgaia(a)gmx.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M config/plugins/interactive_environments/askomics/static/js/askomics.js M config/plugins/interactive_environments/askomics/templates/askomics.mako Log Message: ----------- Merge pull request #1 from dannon/askomics-fixes Small javascript fixes for askomics IE integration Commit: f34e6a1e2e182c10a36172d63740559723058086 https://github.com/galaxyproject/galaxy/commit/f34e6a1e2e182c10a36172d63740… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako Log Message: ----------- Merge pull request #4737 from xgaia/askomics-ie AskOmics Interactive Environment Compare: https://github.com/galaxyproject/galaxy/compare/e27a16953d5f...f34e6a1e2e18

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[galaxyproject/galaxy] 140a0a: Add DELETE /api/jobs/<job_id> as a job cancellatio...
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 140a0a49d3af5f5d6ffaa50cc0cac5b5f4cd1bcc https://github.com/galaxyproject/galaxy/commit/140a0a49d3af5f5d6ffaa50cc0ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-08 (Wed, 08 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/base/populators.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py A test/integration/test_local_job_cancellation.py Log Message: ----------- Add DELETE /api/jobs/<job_id> as a job cancellation API endpoint. Commit: e27a16953d5faadbfa8d2be1e0a09afe4bd7df87 https://github.com/galaxyproject/galaxy/commit/e27a16953d5faadbfa8d2be1e0a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/base/populators.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py A test/integration/test_local_job_cancellation.py Log Message: ----------- Merge pull request #4961 from jmchilton/job_delete_api Add DELETE /api/jobs/<job_id> as a job cancellation API endpoint. Compare: https://github.com/galaxyproject/galaxy/compare/bbd96c435b86...e27a16953d5f

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[galaxyproject/galaxy] a1e912: If installing dev dependencies, do so along side r...
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1e91231aa5dba34c10f039446177d0f55871623 https://github.com/galaxyproject/galaxy/commit/a1e91231aa5dba34c10f03944617… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-02 (Thu, 02 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- If installing dev dependencies, do so along side regular dependencies. Catch conflicts and works faster. Commit: bbd96c435b866a2cab7299fadf0687d7e2c99e3e https://github.com/galaxyproject/galaxy/commit/bbd96c435b866a2cab7299fadf06… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #4903 from jmchilton/dev_at_same_time Install dev and regular dependencies at the same time. Compare: https://github.com/galaxyproject/galaxy/compare/54c6a794e9c6...bbd96c435b86

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[galaxyproject/galaxy] 0a6c29: Add missing ipaddress requirement
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 0a6c2974204b3048456bc7ceba7793ab4774de9f https://github.com/galaxyproject/galaxy/commit/0a6c2974204b3048456bc7ceba77… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add missing ipaddress requirement Broken in https://github.com/galaxyproject/galaxy/pull/4289 . Fix https://github.com/galaxyproject/galaxy/issues/4999 . Commit: 18467e9b2cecb2102d17fd6734f1fb40c5321623 https://github.com/galaxyproject/galaxy/commit/18467e9b2cecb2102d17fd6734f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement [17.09] Add missing ipaddress requirement Compare: https://github.com/galaxyproject/galaxy/compare/b25de8b00316...18467e9b2cec

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[galaxyproject/galaxy] 6c32ed: start writing tests for TDT
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c32edebc1b36136759a055fe3032d51a24f1f68 https://github.com/galaxyproject/galaxy/commit/6c32edebc1b36136759a055fe303… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js A test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- start writing tests for TDT Commit: 7431cb13123f091fc13d5cb2b2756a4bd0726d1f https://github.com/galaxyproject/galaxy/commit/7431cb13123f091fc13d5cb2b275… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- fix TDT's dependency Commit: b0973391640248f29765bacdc0ff0faf68db5f52 https://github.com/galaxyproject/galaxy/commit/b0973391640248f29765bacdc0ff… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-10-17 (Tue, 17 Oct 2017) Changed paths: M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- test successful tour generation Commit: 9d646c605cbab0c59e34379818e2e63f7269e5b6 https://github.com/galaxyproject/galaxy/commit/9d646c605cbab0c59e34379818e2… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- improve the test Commit: 323e1ad64e9f3fa75c32a283b82694474d49ceb0 https://github.com/galaxyproject/galaxy/commit/323e1ad64e9f3fa75c32a283b826… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/jenkins/selenium/Dockerfile M .ci/jenkins/selenium/docker-compose.yml M .ci/jenkins/selenium/galaxy.ini M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt A .ci/tox_envs/flake8/Pipfile A .ci/tox_envs/flake8/requirements.txt A .ci/tox_envs/flake8_imports/Pipfile A .ci/tox_envs/flake8_imports/requirements.txt A .ci/tox_envs/update.sh M .gitignore M .travis.yml M CITATION M Makefile A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/login.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/i18n.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/bibtex.js R client/galaxy/scripts/libs/d3.js R client/galaxy/scripts/libs/jquery.complexify.js R client/galaxy/scripts/libs/jquery/jquery.cookie.js R client/galaxy/scripts/libs/jquery/jquery.js R client/galaxy/scripts/libs/jquery/jquery.migrate.js R client/galaxy/scripts/libs/jquery/jquery.mousewheel.js R client/galaxy/scripts/libs/raven.js R client/galaxy/scripts/libs/require.js R client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/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/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.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/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/job/job-params.js A 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client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/icon-button.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M 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test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_jupyter.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py M test/selenium_tests/test_login.py A test/selenium_tests/test_navigates_galaxy.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py 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tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/extract/liftOver_wrapper.xml M tools/filters/axt_to_lav.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/genomespace/genomespace_importer.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' into tdt_tests # Conflicts: # client/galaxy/scripts/mvc/tool/tool-form-base.js # static/maps/mvc/tool/tool-form-base.js.map # static/scripts/bundled/analysis.bundled.js # static/scripts/bundled/analysis.bundled.js.map # static/scripts/bundled/libs.bundled.js.map # static/scripts/mvc/tool/tool-form-base.js Commit: f419c85955dc9885ef09f77db7e10e5145ef99fd https://github.com/galaxyproject/galaxy/commit/f419c85955dc9885ef09f77db7e1… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-11-01 (Wed, 01 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- add test for TDT Commit: c52ebfca26710b8c9883bbfdba04187d53295427 https://github.com/galaxyproject/galaxy/commit/c52ebfca26710b8c9883bbfdba04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: A test/functional/webhooks/tour_generator M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Improvements for tour generator Selenium tests. - Replace test using Cut1 with two tests each using framework test tools loaded with Selenium tests by default. - Create a symbolic link so that tour generator is configured with default test webhooks. - Establish and use components and navigates_galaxy.py abstractions for tour generation and navigation. - In one of the tool tests actually walk the tour (previously we only verified the initial tour popover). Commit: cecef90915abf0383aed8b56deb4ec237ca9a712 https://github.com/galaxyproject/galaxy/commit/cecef90915abf0383aed8b56deb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh R .ci/tox_envs/flake8/Pipfile R .ci/tox_envs/flake8/requirements.txt R .ci/tox_envs/flake8_imports/Pipfile R .ci/tox_envs/flake8_imports/requirements.txt R .ci/tox_envs/update.sh M .travis.yml M Makefile M README.rst M client/.babelrc M client/galaxy/scripts/admin.toolshed.js M 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client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/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/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M 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test/qunit/tests/popover_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.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 tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into tdt_tests Commit: 9273d7a1c73df1aeb2271dcad6495d1b6fd4f036 https://github.com/galaxyproject/galaxy/commit/9273d7a1c73df1aeb2271dcad649… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- Add screenshots for TDT Selenium tests. Commit: fb91302458f1ab8c1d8dbd59ef0d7ebf29932536 https://github.com/galaxyproject/galaxy/commit/fb91302458f1ab8c1d8dbd59ef0d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- Fix TDT fors ES6 module switchover. Commit: 54c6a794e9c6c3b5e51990875516e026cbac94c0 https://github.com/galaxyproject/galaxy/commit/54c6a794e9c6c3b5e51990875516… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/plugins/webhooks/demo/tour_generator/static/script.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js A test/functional/webhooks/tour_generator M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #4909 from anatskiy/tdt_tests Selenium test for Tool-Describing-Tours Compare: https://github.com/galaxyproject/galaxy/compare/a12b50c08ecf...54c6a794e9c6

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[galaxyproject/galaxy] b4e041: Removed unneeded skip_install tags in tox.ini.
by GitHub 15 Nov '17

15 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4e041d14d4b036c0c6fac3565e92f265d62f079 https://github.com/galaxyproject/galaxy/commit/b4e041d14d4b036c0c6fac3565e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M tox.ini Log Message: ----------- Removed unneeded skip_install tags in tox.ini. Alternative to #4995 thanks to @nsoranzo's detective work. Commit: a12b50c08ecffa383f97342ae53f874be20aff56 https://github.com/galaxyproject/galaxy/commit/a12b50c08ecffa383f97342ae53f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #5011 from jmchilton/remove_skip_install_tox Removed unneeded skip_install tags in tox.ini. Compare: https://github.com/galaxyproject/galaxy/compare/482ff776e596...a12b50c08ecf

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[galaxyproject/galaxy] 68a83c: dataset info: present decoded IDs for admins and a...
by GitHub 14 Nov '17

14 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 68a83ce08395fabf9c388fd0d8fa84cd4ba85e85 https://github.com/galaxyproject/galaxy/commit/68a83ce08395fabf9c388fd0d8fa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M templates/show_params.mako Log Message: ----------- dataset info: present decoded IDs for admins and add peek Commit: 482ff776e59612a5130e8af45661e514764bb0b5 https://github.com/galaxyproject/galaxy/commit/482ff776e59612a5130e8af45661… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #5006 from martenson/decode_for_admins dataset info: present decoded IDs for admins and add peek Compare: https://github.com/galaxyproject/galaxy/compare/39bd5c6a194a...482ff776e596

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