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

[galaxyproject/galaxy] 723628: Add localization defaults to base locale.js, rebui...
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72362815fc0eef44e67e0b00cbbf99513bb09d00 https://github.com/galaxyproject/galaxy/commit/72362815fc0eef44e67e0b00cbbf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/locale.js M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/nls/locale.js Log Message: ----------- Add localization defaults to base locale.js, rebuild client to incorporate latest changes from @manabuishii Commit: ff04384659f80ff5aa156436388012fbd6313efd https://github.com/galaxyproject/galaxy/commit/ff04384659f80ff5aa1564363880… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js M config/galaxy.ini.sample M lib/galaxy/model/__init__.py M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge branch 'dev' into new_localization_manabuishii Commit: 636c30704bad85d1f37a7b3333dc70df2cdafb76 https://github.com/galaxyproject/galaxy/commit/636c30704bad85d1f37a7b3333dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M static/maps/nls/ja/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/ja/locale.js Log Message: ----------- Rebuild with new bundled Japanese translations. Commit: 69c4823f581657660efe649d224de45cb484c4c7 https://github.com/galaxyproject/galaxy/commit/69c4823f581657660efe649d224d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/locale.js M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js Log Message: ----------- Merge pull request #4309 from dannon/new_localization_manabuishii Add localization defaults to base locale.js, rebuild client Compare: https://github.com/galaxyproject/galaxy/compare/68e6cdbe81cd...69c4823f5816

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[galaxyproject/usegalaxy-playbook] 437643: Return node names on swarm scale destruction
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 437643a11e6b5dfc33099a6fdf8864fa620b3326 https://github.com/galaxyproject/usegalaxy-playbook/commit/437643a11e6b5dfc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M roles/usegalaxy_swarmscale/files/instance Log Message: ----------- Return node names on swarm scale destruction

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[galaxyproject/usegalaxy-playbook] 333669: Instruct GIE launcher not to attempt to use volume...
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 33366949a7e2a5eae219a108899a305670dab73d https://github.com/galaxyproject/usegalaxy-playbook/commit/33366949a7e2a5ea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M production/group_vars/galaxywebservers.yml Log Message: ----------- Instruct GIE launcher not to attempt to use volumes Commit: 9028505708ccd65ae43ad2e01e694a8ca066b48b https://github.com/galaxyproject/usegalaxy-playbook/commit/9028505708ccd65a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Downtime banner Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/cedb92eef64b...…

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[galaxyproject/usegalaxy-playbook] 4dd07f: Update Jupyter version in Galaxy config for Test
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4dd07fe64f3d15501701f84950ea46ca82f43b03 https://github.com/galaxyproject/usegalaxy-playbook/commit/4dd07fe64f3d1550… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Update Jupyter version in Galaxy config for Test

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[galaxyproject/usegalaxy-playbook] cedb92: Switch Main to Jupyter 17.05.1 image
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cedb92eef64b06c061ee831e3686f0e09a45e592 https://github.com/galaxyproject/usegalaxy-playbook/commit/cedb92eef64b06c0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M production/group_vars/galaxywebservers.yml Log Message: ----------- Switch Main to Jupyter 17.05.1 image

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[galaxyproject/usegalaxy-playbook] bdcfa1: Get swarm scale / swarm manager working for Test, ...
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bdcfa1009eb413827f509c6c1787a6418f6cb9f3 https://github.com/galaxyproject/usegalaxy-playbook/commit/bdcfa1009eb41382… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-12 (Wed, 12 Jul 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/group_vars/galaxyservers/vars.yml M roles/usegalaxy_swarmscale/files/instance M roles/usegalaxy_swarmscale/files/inventory.spawn Log Message: ----------- Get swarm scale / swarm manager working for Test, update Test to new GIE images (Jupyter 17.05.1)

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[galaxyproject/galaxy] 2e2d46: Update Japanese translation
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e2d46491ff4ced0a5b9c7999c442b8b29bd4fc5 https://github.com/galaxyproject/galaxy/commit/2e2d46491ff4ced0a5b9c7999c44… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js Log Message: ----------- Update Japanese translation Commit: 26ef9b02c814cca93b2278be6e462f7d6b8dca2d https://github.com/galaxyproject/galaxy/commit/26ef9b02c814cca93b2278be6e46… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js Log Message: ----------- Update Localization Edit history Annotaion was used in locale.js But it must be 'Edit history annotation' . It is written in client/galaxy/scripts/mvc/history/history-view-edit.js Commit: 76fa748c47901195379bfd2bb40f9ee5080cdf90 https://github.com/galaxyproject/galaxy/commit/76fa748c47901195379bfd2bb40f… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js Log Message: ----------- Localization Admin Commit: 68e6cdbe81cd5d310e770248fcd6aeef05ff5123 https://github.com/galaxyproject/galaxy/commit/68e6cdbe81cd5d310e770248fcd6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js Log Message: ----------- Merge pull request #4304 from manabuishii/nls_ja_locale Update Japanese translation Compare: https://github.com/galaxyproject/galaxy/compare/641a268d7137...68e6cdbe81cd

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[galaxyproject/galaxy] 8df7b3: Update __init__.py
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8df7b309a977eed9d5926a28afe90a1cf4f07580 https://github.com/galaxyproject/galaxy/commit/8df7b309a977eed9d5926a28afe9… Author: cche <cche(a)users.noreply.github.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Update __init__.py Commit: e4ab9b08c885eb5c6be2318e6b67a1975e2db408 https://github.com/galaxyproject/galaxy/commit/e4ab9b08c885eb5c6be2318e6b67… Author: Cristian <cche(a)users.noreply.github.com> Date: 2017-06-30 (Fri, 30 Jun 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Correct indent and add a break Commit: 8a309ceca454f5b74566d33fbde28121d961eea0 https://github.com/galaxyproject/galaxy/commit/8a309ceca454f5b74566d33fbde2… Author: Cristian <> Date: 2017-06-30 (Fri, 30 Jun 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Moved the code up and added an explanatory comment. Also added spaces within the parens to match the existing style. Commit: 641a268d713767ac11dbddab1e9e7159b5b8d111 https://github.com/galaxyproject/galaxy/commit/641a268d713767ac11dbddab1e9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #4268 from cche/cche-import-hist-withsubdir Importing old exported histories failing Compare: https://github.com/galaxyproject/galaxy/compare/db486b50ef45...641a268d7137

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[galaxyproject/galaxy] d10758: Merge pull request #3077 from galaxyproject/releas...
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d10758a4f22daa24bdf55863f360493a4a3902f7 https://github.com/galaxyproject/galaxy/commit/d10758a4f22daa24bdf55863f360… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/ui/ui-modal.js M config/galaxy.ini.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js M templates/user/index.mako M templates/webapps/galaxy/workflow/run.mako M test/shed_functional/functional/test_1400_review_migration_stages.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #3077 from galaxyproject/release_16.07 [master] bring master on par with release_16.07 Commit: 378ed53a33eee02c3620310c7245e7a85d279427 https://github.com/galaxyproject/galaxy/commit/378ed53a33eee02c3620310c7245… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt A .ci/validate_test_tools.sh M .gitignore M .travis.yml M CONTRIBUTORS.md M LICENSE.txt M Makefile M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bbi/bigwig.js A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js A client/galaxy/scripts/libs/bbi/jszlib.js A client/galaxy/scripts/libs/bbi/spans.js A client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js A client/galaxy/scripts/mvc/base/controlled-fetch-collection.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.js M client/galaxy/scripts/mvc/dataset/data.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-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-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/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.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-model.js A 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/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M 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client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/scripts/utils/utils.js A client/galaxy/scripts/viz/bbi-data-manager.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less A client/galaxy/style/less/collection.less R client/galaxy/style/less/collections.less A client/galaxy/style/less/dataset.less A client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less M client/galaxy/style/less/ui.less A client/galaxy/style/less/ui/error-modal.less M 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test/unit/tools/test_tool_external_files.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.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 test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.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_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.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_split_by_species.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/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.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/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.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_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_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 tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge branch 'release_16.10' Commit: 8b538f17feb17eba11b3025a2dfb3ba35414a78e https://github.com/galaxyproject/galaxy/commit/8b538f17feb17eba11b3025a2dfb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/plugins/tours/core.history.yaml M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/output_collect.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_tools.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge branch 'release_16.10' Commit: 3a2ff46c28172ef78510f4bea2f4be75ce660667 https://github.com/galaxyproject/galaxy/commit/3a2ff46c28172ef78510f4bea2f4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js A client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/charts/webpack.config.js M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js A display_applications/igv/genome_fasta.xml M doc/schema_template.md M doc/source/admin/dependency_resolvers.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M doc/source/dev/faq.rst M 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test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_mapper.py M test/unit/test_sockets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/workflow_support.py M tools/data_source/fetch.py R tools/filters/gff/sort_gtf.py M tools/plotting/bar_chart.xml M tox.ini Log Message: ----------- Merge branch 'release_17.01' Commit: 52b5e62de498f08ccd55f792d555c884f8bd6e98 https://github.com/galaxyproject/galaxy/commit/52b5e62de498f08ccd55f792d555… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M display_applications/igv/bigwig.xml M doc/source/releases/17.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/runners/__init__.py M 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templates/webapps/galaxy/user/manage_info.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' Commit: dd439530509f12ede24f8e9763f2bdb5314e2c13 https://github.com/galaxyproject/galaxy/commit/dd439530509f12ede24f8e9763f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' Commit: 7e64fa395c6c56a0973f56ecc1aa615f15d9fe80 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tools/next_gen_conversion/fastq_gen_conv.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge branch 'release_17.05' Commit: d1681153bece3ed294e5b305e18d822745638b5b https://github.com/galaxyproject/galaxy/commit/d1681153bece3ed294e5b305e18d… Author: Ashok Varadharajan <ashvark(a)users.noreply.github.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M CONTRIBUTING.md A SECURITY_POLICY.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M 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static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.library.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/js-app.mako M 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A test-data/5_Ig-like.gff M test/api/test_dataset_collections.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_config_options_users.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/wc_gnu.xml Log Message: ----------- Merge pull request #1 from galaxyproject/dev Merging Commit: 320da989b19a281542d47fe5ef8064aac5db2576 https://github.com/galaxyproject/galaxy/commit/320da989b19a281542d47fe5ef80… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Log Message: ----------- Merge remote-tracking branch 'upstream/master' into dev Commit: ccf12bb26157353769b25566df31ff2189c9c686 https://github.com/galaxyproject/galaxy/commit/ccf12bb26157353769b25566df31… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/model/__init__.py Log Message: ----------- allowing 'real_system_username' to accept a common-system-user to run all the jobs Commit: db486b50ef459a99356ab67c7c69e25be2f165e9 https://github.com/galaxyproject/galaxy/commit/db486b50ef459a99356ab67c7c69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4294 from ashvark/real_system_username Submitting the galaxy jobs as a predefined system user: using 'real_system_username' Compare: https://github.com/galaxyproject/galaxy/compare/feefa03ba234...db486b50ef45

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[galaxyproject/galaxy] 6c4936: Localization support for Tool Help
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c493693c1f610653bcd3bbc0e75c4848fbc81a0 https://github.com/galaxyproject/galaxy/commit/6c493693c1f610653bcd3bbc0e75… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Localization support for Tool Help Commit: e5383b8fe42eab9cb22368a9eb8c5ebd082d1843 https://github.com/galaxyproject/galaxy/commit/e5383b8fe42eab9cb22368a9eb8c… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- forget l Commit: feefa03ba2347f57bc37838ba695e9c28a822191 https://github.com/galaxyproject/galaxy/commit/feefa03ba2347f57bc37838ba695… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #4306 from manabuishii/patch-6 Localization support for Tool Help Compare: https://github.com/galaxyproject/galaxy/compare/bf63ea2bdc48...feefa03ba234

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