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December 2015
- 1 participants
- 195 discussions
05 Dec '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bab7ae099845f4503a2e41c939abc2aca9dc7a66
https://github.com/galaxyproject/galaxy/commit/bab7ae099845f4503a2e41c939ab…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M test/base/twilltestcase.py
Log Message:
-----------
Improved logging related tool test timeouts.
There are transient failures of maxseconds.xml's tool test on Jenkins that I can't reproduce locally, hopefully improved logging will help.
https://jenkins.galaxyproject.org/job/docker-framework/1309/testReport/juni…
Commit: b0c1cd7460f13075c565750298f9d4c3cb89bb80
https://github.com/galaxyproject/galaxy/commit/b0c1cd7460f13075c565750298f9…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-05 (Sat, 05 Dec 2015)
Changed paths:
M test/base/twilltestcase.py
Log Message:
-----------
Merge pull request #1243 from jmchilton/maxseconds_debug
Improved logging related tool test timeouts.
Compare: https://github.com/galaxyproject/galaxy/compare/f7a2acdcabdf...b0c1cd7460f1
1
0
05 Dec '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0924891e31f3f215323fe7030e0d6c167f596878
https://github.com/galaxyproject/galaxy/commit/0924891e31f3f215323fe7030e0d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M test/qunit/test-common.js
Log Message:
-----------
Fix up merge issue with double underscore shim.
Commit: f7a2acdcabdfb0d2368e00c4959712bf7d5c98f2
https://github.com/galaxyproject/galaxy/commit/f7a2acdcabdfb0d2368e00c49597…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-05 (Sat, 05 Dec 2015)
Changed paths:
M test/qunit/test-common.js
Log Message:
-----------
Merge pull request #1246 from jmchilton/test-commons
Fix up merge issue with double underscore shim.
Compare: https://github.com/galaxyproject/galaxy/compare/9f8eb465e718...f7a2acdcabdf
1
0
05 Dec '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0c03f69c3952ab4dda8c09b39bf5caea97cd10d6
https://github.com/galaxyproject/galaxy/commit/0c03f69c3952ab4dda8c09b39bf5…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-07-17 (Fri, 17 Jul 2015)
Changed paths:
A client/galaxy/scripts/apps/history-app.js
A client/galaxy/scripts/apps/libs.js
A client/galaxy/scripts/galaxy-app-webpack.js
A client/galaxy/scripts/libs/common-libs.js
A client/galaxy/scripts/utils/webpack-localization.js
A client/webpack.config.js
M lib/galaxy/web/base/controller.py
A static/maps/apps/history-app.js.map
A static/maps/apps/libs.js.map
A static/maps/galaxy-app-webpack.js.map
A static/maps/libs/common-libs.js.map
A static/maps/utils/webpack-localization.js.map
A static/scripts/apps/history-app.js
A static/scripts/apps/libs.js
A static/scripts/bundled/common.js
A static/scripts/bundled/history.bundled.js
A static/scripts/bundled/libs.bundled.js
A static/scripts/galaxy-app-webpack.js
A static/scripts/libs/common-libs.js
A static/scripts/utils/webpack-localization.js
A templates/js-app.mako
Log Message:
-----------
Client build, webpack: prototype commit
Commit: 25770f4c7cf8c7dfb4f50692fbe2154b4053a484
https://github.com/galaxyproject/galaxy/commit/25770f4c7cf8c7dfb4f50692fbe2…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-07-17 (Fri, 17 Jul 2015)
Changed paths:
M client/galaxy/scripts/galaxy-app-base.js
M client/galaxy/scripts/galaxy-app-webpack.js
M lib/galaxy/managers/configuration.py
M lib/galaxy/web/base/controller.py
M static/maps/galaxy-app-base.js.map
M static/maps/galaxy-app-webpack.js.map
M static/scripts/bundled/history.bundled.js
M static/scripts/galaxy-app-base.js
M static/scripts/galaxy-app-webpack.js
Log Message:
-----------
Client build, webpack: move app-webpack closer to app-base for replacement/inheritance, fix bootstrapping of configuration and use managers
Commit: 1fd38fb3ee467473d5326ef8c197cedcd9472d53
https://github.com/galaxyproject/galaxy/commit/1fd38fb3ee467473d5326ef8c197…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-07-21 (Tue, 21 Jul 2015)
Changed paths:
M client/package.json
M static/scripts/bundled/history.bundled.js
Log Message:
-----------
Client build: update webpack versions in package.json; recompile
Commit: 0235eceb57101d03f6027a28980535a4accd02a6
https://github.com/galaxyproject/galaxy/commit/0235eceb57101d03f6027a289805…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-10-23 (Fri, 23 Oct 2015)
Changed paths:
A .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
R .ci/pep8_sources.txt
M .gitignore
A CODE_OF_CONDUCT.md
M CONTRIBUTING.md
M README.rst
M client/GruntFile.js
M client/README.md
M client/bower.json
M client/galaxy/scripts/galaxy-app-base.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.menu.js
M client/galaxy/scripts/galaxy.panels.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/farbtastic.js
M client/galaxy/scripts/libs/handlebars.runtime.js
A client/galaxy/scripts/libs/jquery.sparklines.js
M client/galaxy/scripts/libs/jquery/jqtouch.js
M client/galaxy/scripts/libs/jquery/jquery.dynatree.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
A client/galaxy/scripts/mvc/app/app-analysis.js
A client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/scripts/mvc/base-mvc.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/list-of-pairs-collection-creator.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/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
A client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-panel-edit-current.js
M client/galaxy/scripts/mvc/history/history-panel-edit.js
M client/galaxy/scripts/mvc/history/history-panel.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-folderlist-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/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M client/galaxy/scripts/mvc/tools/tools-form-workflow.js
M client/galaxy/scripts/mvc/tools/tools-form.js
M client/galaxy/scripts/mvc/tools/tools-jobs.js
R client/galaxy/scripts/mvc/ui/ui-button-check.js
R client/galaxy/scripts/mvc/ui/ui-button-menu.js
A 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-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
A client/galaxy/scripts/mvc/upload/composite/composite-row.js
A client/galaxy/scripts/mvc/upload/composite/composite-view.js
A client/galaxy/scripts/mvc/upload/default/default-row.js
A 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-model.js
R client/galaxy/scripts/mvc/upload/upload-row.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
A client/galaxy/scripts/reports_webapp/run_stats.js
R client/galaxy/scripts/templates/compile_templates.py
M client/galaxy/scripts/templates/compiled/panel_section.js
M client/galaxy/scripts/templates/compiled/tool_form.js
M client/galaxy/scripts/templates/compiled/tool_link.js
M client/galaxy/scripts/templates/compiled/tool_search.js
M client/galaxy/scripts/utils/config.js
A client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/list-item.less
A client/galaxy/style/less/reports.less
M client/galaxy/style/less/trackster.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/galaxy/style/source_material/circle.py
M client/grunt-tasks/install-libs.js
M client/grunt-tasks/scripts.js
M client/grunt-tasks/style.js
A client/grunt-tasks/templates.js
M client/package.json
M config/auth_conf.xml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M config/plugins/interactive_environments/ipython/templates/ipython.mako
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
A config/plugins/visualizations/graphviz/README.md
A config/plugins/visualizations/graphviz/config/graphviz.xml
A config/plugins/visualizations/graphviz/static/css/style.css
A config/plugins/visualizations/graphviz/static/img/15xvbd5.png
A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png
A config/plugins/visualizations/graphviz/static/js/collapse.js
A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js
A config/plugins/visualizations/graphviz/static/js/graphVis.js
A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js
A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js
A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js
A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js
A config/plugins/visualizations/graphviz/templates/graphviz.mako
M config/plugins/visualizations/trackster/config/trackster.xml
M config/tool_data_table_conf.xml.sample
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M create_db.sh
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/cleanup_datasets.py
M cron/parse_builds_3_sites.py
R dist-eggs.ini
M doc/patch.py
A doc/source/admin/index.rst
A doc/source/admin/interactive_environments.png
A doc/source/admin/interactive_environments.rst
A doc/source/admin/interactive_environments.svg
A doc/source/admin/interactive_environments_success.png
A doc/source/admin/useful_scripts.rst
A doc/source/api/guidelines.rst
A doc/source/api/quickstart.rst
M doc/source/api_doc.rst
M doc/source/conf.py
A doc/source/dev/faq.rst
A doc/source/dev/index.rst
M doc/source/index.rst
R doc/source/lib/galaxy.jobs.runners.lwr_client.rst
R doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst
R doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst
M doc/source/lib/galaxy.jobs.runners.rst
A doc/source/project/issues.rst
M doc/source/project/organization.rst
A doc/source/releases/15.07.rst
M doc/source/releases/15.07_announce.rst
A doc/source/releases/15.10_announce.rst
M doc/source/releases/_header.rst
M doc/source/releases/index.rst
A doc/source/ts_api_doc.rst
R eggs.ini
M lib/galaxy/__init__.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
A lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/coverage.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/1.gg
A lib/galaxy/datatypes/test/oxli_countgraph.oxlicg
A lib/galaxy/datatypes/test/oxli_graphlabels.oxligl
A lib/galaxy/datatypes/test/oxli_nodegraph.oxling
A lib/galaxy/datatypes/test/oxli_stoptags.oxlist
A lib/galaxy/datatypes/test/oxli_subset.oxliss
A lib/galaxy/datatypes/test/oxli_tagset.oxlits
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
A lib/galaxy/dependencies/__init__.py
A lib/galaxy/dependencies/conditional-requirements.txt
A lib/galaxy/dependencies/dev-requirements.txt
A lib/galaxy/dependencies/requirements.txt
M lib/galaxy/eggs/__init__.py
R lib/galaxy/eggs/dist.py
R lib/galaxy/eggs/scramble.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/__init__.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/datasets.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/local.py
R lib/galaxy/jobs/runners/lwr.py
R lib/galaxy/jobs/runners/lwr_client/__init__.py
R lib/galaxy/jobs/runners/lwr_client/action_mapper.py
R lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py
R lib/galaxy/jobs/runners/lwr_client/amqp_exchange_factory.py
R lib/galaxy/jobs/runners/lwr_client/client.py
R lib/galaxy/jobs/runners/lwr_client/config_util.py
R lib/galaxy/jobs/runners/lwr_client/decorators.py
R lib/galaxy/jobs/runners/lwr_client/destination.py
R lib/galaxy/jobs/runners/lwr_client/interface.py
R lib/galaxy/jobs/runners/lwr_client/job_directory.py
R lib/galaxy/jobs/runners/lwr_client/manager.py
R lib/galaxy/jobs/runners/lwr_client/object_client.py
R lib/galaxy/jobs/runners/lwr_client/path_mapper.py
R lib/galaxy/jobs/runners/lwr_client/setup_handler.py
R lib/galaxy/jobs/runners/lwr_client/staging/__init__.py
R lib/galaxy/jobs/runners/lwr_client/staging/down.py
R lib/galaxy/jobs/runners/lwr_client/staging/up.py
R lib/galaxy/jobs/runners/lwr_client/transport/__init__.py
R lib/galaxy/jobs/runners/lwr_client/transport/curl.py
R lib/galaxy/jobs/runners/lwr_client/transport/standard.py
R lib/galaxy/jobs/runners/lwr_client/util.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handler_factory.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/main.py
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/orm/__init__.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/model/orm/logging_connection_proxy.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/model/search.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/model/tool_shed_install/mapping.py
M lib/galaxy/model/tool_shed_install/migrate/check.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/openid/providers.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/stock.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/wrappers.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
M lib/galaxy/util/bunch.py
M lib/galaxy/util/dbkeys.py
M lib/galaxy/util/debugging.py
M lib/galaxy/util/dictobj.py
M lib/galaxy/util/expressions.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/log/__init__.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/lrucache.py
M lib/galaxy/util/none_like.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/plugin_config.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/specs.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/template.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/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/cigar.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/base/controller.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/buildapp.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/__init__.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/profile.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/middleware/request_id.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/static.py
A lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/params.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/galaxy/api/annotations.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/extended_metadata.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/groups.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/item_tags.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/request_types.py
M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/samples.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/biostar.py
R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/error.py
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/external_services.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/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests.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/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
R lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/__init__.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/reports/config.py
A lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/query.py
M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/__init__.py
M lib/galaxy/webapps/tool_shed/api/authenticate.py
M lib/galaxy/webapps/tool_shed/api/categories.py
A lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/webapps/tool_shed/model/migrate/check.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/galaxy/webapps/tool_shed/search/repo_search.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
A lib/galaxy/webapps/util.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/galaxy/workflow/run.py
M lib/galaxy_ext/metadata/__init__.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/galaxy_utils/sequence/fasta.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/sequence.py
M lib/galaxy_utils/sequence/transform.py
M lib/galaxy_utils/sequence/vcf.py
M lib/log_tempfile.py
M lib/mimeparse.py
R lib/pkg_resources.py
M lib/psyco_full.py
M lib/pulsar/client/action_mapper.py
M lib/pulsar/client/amqp_exchange.py
M lib/pulsar/client/amqp_exchange_factory.py
M lib/pulsar/client/client.py
M lib/pulsar/client/config_util.py
M lib/pulsar/client/decorators.py
M lib/pulsar/client/interface.py
M lib/pulsar/client/manager.py
M lib/pulsar/client/staging/__init__.py
M lib/pulsar/client/staging/down.py
M lib/pulsar/client/staging/up.py
M lib/pulsar/client/transport/curl.py
M lib/pulsar/client/transport/poster.py
M lib/pulsar/client/transport/requests.py
M lib/pulsar/client/util.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/dependencies/tool/tag_attribute_handler.py
M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py
M lib/tool_shed/galaxy_install/dependency_display.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py
M lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M lib/tool_shed/galaxy_install/utility_containers/__init__.py
M lib/tool_shed/grids/admin_grids.py
M lib/tool_shed/grids/repository_grid_filter_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/managers/groups.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/repository_types/metadata.py
M lib/tool_shed/repository_types/repository_suite_definition.py
M lib/tool_shed/repository_types/tool_dependency_definition.py
M lib/tool_shed/repository_types/util.py
M lib/tool_shed/scripts/api/add_repository_registry_entry.py
M lib/tool_shed/scripts/api/common.py
M lib/tool_shed/scripts/api/create_categories.py
M lib/tool_shed/scripts/api/create_users.py
M lib/tool_shed/scripts/api/export.py
M lib/tool_shed/scripts/api/get_filtered_repository_revisions.py
M lib/tool_shed/scripts/api/import_capsule.py
M lib/tool_shed/scripts/api/remove_repository_registry_entry.py
M lib/tool_shed/scripts/api/reset_metadata_on_repositories.py
M lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
M lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py
M lib/tool_shed/scripts/check_repositories_for_functional_tests.py
M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
M lib/tool_shed/scripts/clean_up_tool_dependency_directory.py
M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/container_util.py
M lib/tool_shed/util/encoding_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/review_util.py
M lib/tool_shed/util/search_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/xml_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M manage_db.sh
M manage_tools.sh
M requirements.txt
M run.sh
R run_functional_tests.sh
M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/api/common.py
A scripts/api/library_upload_dir.py
A scripts/auth/pam_auth_helper.py
M scripts/bootstrap_history.py
A scripts/bootstrap_history_announce_template.rst
M scripts/build_toolbox.py
M scripts/build_universe_config.py
R scripts/check_eggs.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
R scripts/dist-scramble.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/edam_mapping.py
R scripts/egg_packager_template.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
R scripts/fetch_eggs.py
M scripts/functional_tests.py
M scripts/get_platforms.py
M scripts/helper.py
R scripts/make_egg_packager.py
M scripts/manage_db.py
M scripts/manage_tools.py
M scripts/metagenomics/convert_title.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_table.py
M scripts/migrate_tools/migrate_tools.py
M scripts/nosetests.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/paster.py
M scripts/runtime_stats.py
R scripts/scramble.py
R scripts/scramble/lib/scramble_lib.py
R scripts/scramble/patches/Cheetah/SetupConfig.py
R scripts/scramble/patches/MySQL_python/site.cfg
R scripts/scramble/patches/PasteScript/setup.py
R scripts/scramble/patches/python_daemon/setup.py
R scripts/scramble/scripts/DRMAA_python-macosx.py
R scripts/scramble/scripts/DRMAA_python-solaris.py
R scripts/scramble/scripts/DRMAA_python.py
R scripts/scramble/scripts/MySQL_python-solaris.py
R scripts/scramble/scripts/MySQL_python.py
R scripts/scramble/scripts/PyRods.py
R scripts/scramble/scripts/bx_python-solaris.py
R scripts/scramble/scripts/generic.py
R scripts/scramble/scripts/pbs_python.py
R scripts/scramble/scripts/psycopg2-linux.py
R scripts/scramble/scripts/psycopg2-macosx.py
R scripts/scramble/scripts/psycopg2-solaris.py
R scripts/scramble/scripts/psycopg2.py
R scripts/scramble/scripts/pysam-solaris.py
R scripts/scramble/scripts/pysqlite.py
M scripts/set_dataset_sizes.py
M scripts/set_metadata.py
M scripts/set_user_disk_usage.py
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
R scripts/test_dist_egg.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tools/maf/check_loc_file.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M set_metadata.sh
M setup.cfg
R static/help.css
R static/help.html
R static/help.rst
R static/images/SetAttr.png
R static/images/SetGenome.png
R static/images/brochure.pdf
R static/images/galaxy.png
R static/images/galaxyLogo_small.png
R static/images/lock.jpg
R static/images/qk/quickie1_small.png
R static/images/qk/quickie2_small.png
R static/images/qk/quickie3_small.png
R static/images/qk/quickie4_small.png
R static/images/qk/quickie5_small.png
R static/images/qk/quickie6_small.png
R static/images/qk/quickie7_small.png
R static/images/screencast.png
R static/images/sequencer.png
R static/images/tools.gif
R static/images/toolsExpandingMenu.gif
R static/images/welcomePhoto.jpg
M static/maps/galaxy-app-base.js.map
M static/maps/galaxy.library.js.map
M static/maps/galaxy.menu.js.map
M static/maps/galaxy.panels.js.map
M static/maps/libs/d3.js.map
M static/maps/libs/farbtastic.js.map
M static/maps/libs/handlebars.runtime.js.map
A static/maps/libs/jquery.sparklines.js.map
M static/maps/libs/jquery/jqtouch.js.map
M static/maps/libs/jquery/jquery.dynatree.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/tracekit.js.map
A static/maps/mvc/app/app-analysis.js.map
A static/maps/mvc/app/app-view.js.map
M static/maps/mvc/base-mvc.js.map
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M static/maps/mvc/collection/collection-model.js.map
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R static/maps/mvc/ui/ui-button-menu.js.map
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A static/scripts/libs/jquery.sparklines.js
M static/scripts/libs/jquery/jqtouch.js
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M static/scripts/libs/raven.js
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R static/scripts/templates/compile_templates.py
M static/scripts/templates/compiled/panel_section.js
M static/scripts/templates/compiled/tool_form.js
M static/scripts/templates/compiled/tool_link.js
M static/scripts/templates/compiled/tool_search.js
R static/scripts/templates/panel_section.handlebars
R static/scripts/templates/tool_form.handlebars
R static/scripts/templates/tool_link.handlebars
R static/scripts/templates/tool_search.handlebars
M static/scripts/utils/config.js
A static/scripts/utils/query-string-parsing.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/autocomplete_tagging.css
M static/style/blue/base.css
M static/style/blue/circster.css
R static/style/blue/dynatree_skin/cbChecked.gif
R static/style/blue/dynatree_skin/cbChecked_hover.gif
R static/style/blue/dynatree_skin/cbIntermediate.gif
R static/style/blue/dynatree_skin/cbIntermediate_hover.gif
R static/style/blue/dynatree_skin/cbUnchecked.gif
R static/style/blue/dynatree_skin/cbUnchecked_hover.gif
R static/style/blue/dynatree_skin/customDoc1.gif
R static/style/blue/dynatree_skin/customFolder1.gif
A static/style/blue/dynatree_skin/icons-rtl.gif
A static/style/blue/dynatree_skin/icons.gif
A static/style/blue/dynatree_skin/loading.gif
R static/style/blue/dynatree_skin/ltD_ne.gif
R static/style/blue/dynatree_skin/ltD_nes.gif
R static/style/blue/dynatree_skin/ltDoc.gif
R static/style/blue/dynatree_skin/ltError.gif
R static/style/blue/dynatree_skin/ltFld.gif
R static/style/blue/dynatree_skin/ltFld_o.gif
R static/style/blue/dynatree_skin/ltL_.gif
R static/style/blue/dynatree_skin/ltL_ne.gif
R static/style/blue/dynatree_skin/ltL_nes.gif
R static/style/blue/dynatree_skin/ltL_ns.gif
R static/style/blue/dynatree_skin/ltM_ne.gif
R static/style/blue/dynatree_skin/ltM_nes.gif
R static/style/blue/dynatree_skin/ltP_ne.gif
R static/style/blue/dynatree_skin/ltP_nes.gif
R static/style/blue/dynatree_skin/ltWait.gif
R static/style/blue/dynatree_skin/rbChecked.gif
R static/style/blue/dynatree_skin/rbChecked_hover.gif
R static/style/blue/dynatree_skin/rbIntermediate.gif
R static/style/blue/dynatree_skin/rbIntermediate_hover.gif
R static/style/blue/dynatree_skin/rbUnchecked.gif
R static/style/blue/dynatree_skin/rbUnchecked_hover.gif
M static/style/blue/dynatree_skin/ui.dynatree.css
A static/style/blue/dynatree_skin/vline-rtl.gif
A static/style/blue/dynatree_skin/vline.gif
M static/style/blue/embed_item.css
M static/style/blue/iphone.css
M static/style/blue/library.css
M static/style/blue/masthead.css
A static/style/blue/reports.css
M static/style/blue/sprite-fugue.png
M static/style/blue/sprite-history-buttons.png
M static/style/blue/sprite-history-states.png
M static/style/blue/trackster.css
R static/welcome.rst
M templates/admin/requests/select_datasets_to_transfer.mako
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
A templates/page_base.mako
M templates/search/index.mako
M templates/show_params.mako
M templates/sorting_base.mako
A templates/spark_base.mako
M templates/user/login.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/sanitize_whitelist.mako
R templates/webapps/galaxy/cloud/index.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/data_manager/view_job.mako
M templates/webapps/galaxy/galaxy.masthead.mako
A templates/webapps/galaxy/history/as_xml.mako
M templates/webapps/galaxy/history/copy.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/history/structure.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/history/view_multiple.mako
M templates/webapps/galaxy/library/common/ldda_info.mako
M templates/webapps/galaxy/library/common/ldda_permissions.mako
R templates/webapps/galaxy/root/history.mako
R templates/webapps/galaxy/root/history_as_xml.mako
M templates/webapps/galaxy/root/index.mako
R templates/webapps/galaxy/root/tool_menu.mako
A templates/webapps/galaxy/root/tool_runner.mako
R templates/webapps/galaxy/tool_executed.mako
R templates/webapps/galaxy/tool_form.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/reports/base_panels.mako
M templates/webapps/reports/index.mako
M templates/webapps/reports/job_info.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/registered_users_specified_date.mako
M templates/webapps/reports/registered_users_specified_month.mako
M templates/webapps/reports/requests_per_month_all.mako
M templates/webapps/reports/requests_per_user.mako
M templates/webapps/reports/requests_user_per_month.mako
A templates/webapps/reports/run_stats.mako
M templates/webapps/reports/system.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
A templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
R templates/webapps/tool_shed/message.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
A test-data/1.RData
A test-data/3.bam
M test/api/helpers.py
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_histories.py
M test/api/test_jobs.py
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/yaml_to_workflow.py
M test/base/asserts/__init__.py
M test/base/instrument.py
M test/base/interactor.py
M test/base/nose_util.py
M test/base/test_data.py
M test/base/test_db_util.py
A test/base/test_logging.py
M test/base/tool_shed_util.py
M test/base/twilltestcase.py
M test/casperjs/anon-history-tests.js
M test/casperjs/api-anon-history-permission-tests.js
M test/casperjs/api-hda-tests.js
M test/casperjs/api-history-permission-tests.js
M test/casperjs/api-history-tests.js
M test/casperjs/casperjs_runner.py
M test/casperjs/hda-state-tests.js
M test/casperjs/history-panel-tests.js
M test/casperjs/modules/historypanel.js
M test/casperjs/server_env.py
M test/docker/README.md
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
M test/functional/test_admin_features.py
M test/functional/test_data_managers.py
M test/functional/test_data_security.py
M test/functional/test_get_data.py
M test/functional/test_library_features.py
M test/functional/test_library_security.py
M test/functional/test_library_templates.py
M test/functional/test_metadata_editing.py
M test/functional/test_sample_tracking.py
M test/functional/test_toolbox.py
M test/functional/test_ucsc_table_browser.py
M test/functional/test_user_info.py
A test/functional/tool-data/fasta_indexes.loc
M test/functional/tool-data/sample_tool_data_tables.xml
A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
A test/functional/tools/collection_creates_dynamic_nested.xml
A test/functional/tools/collection_creates_list_of_pairs.xml
R test/functional/tools/compare_bam_as_sam.xml
A test/functional/tools/dbkey_filter_input.xml
A test/functional/tools/dbkey_filter_multi_input.xml
M test/functional/tools/disambiguate_cond.xml
M test/functional/tools/metadata_bam.xml
M test/functional/tools/min_repeat.xml
M test/functional/tools/multi_data_param.xml
M test/functional/tools/multi_output_configured.xml
A test/functional/tools/output_collection_filter.xml
M test/functional/tools/output_format.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/simple_constructs.yml
M test/functional/tools/validation_repeat.xml
M test/functional/workflow.py
M test/install_and_test_tool_shed_repositories/base/test_db_util.py
M test/install_and_test_tool_shed_repositories/base/twilltestcase.py
M test/install_and_test_tool_shed_repositories/base/util.py
M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
M test/manual/workflows_scaling.py
M test/qunit/README.txt
M test/qunit/package.json
A test/qunit/test-app.js
M test/qunit/test-common.js
A test/qunit/test-data/bootstrapped.js
A test/qunit/test-data/fakeserver.js
A test/qunit/tests/upload_dialog_tests.html
A test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/tool_shed/base/test_db_util.py
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_0000_basic_repository_features.py
M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_0020_basic_repository_dependencies.py
M test/tool_shed/functional/test_0030_repository_dependency_revisions.py
M test/tool_shed/functional/test_0040_repository_circular_dependencies.py
M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_0060_workflows.py
M test/tool_shed/functional/test_0070_invalid_tool.py
M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
M test/tool_shed/functional/test_0090_tool_search.py
M test/tool_shed/functional/test_0100_complex_repository_dependencies.py
M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_0130_datatype_converters.py
M test/tool_shed/functional/test_0140_tool_help_images.py
M test/tool_shed/functional/test_0150_prior_installation_required.py
M test/tool_shed/functional/test_0160_circular_prior_installation_required.py
M test/tool_shed/functional/test_0170_complex_prior_installation_required.py
M test/tool_shed/functional/test_0300_reset_all_metadata.py
M test/tool_shed/functional/test_0310_hg_push_from_api.py
M test/tool_shed/functional/test_0400_repository_component_reviews.py
M test/tool_shed/functional/test_0410_repository_component_review_access_control.py
M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
M test/tool_shed/functional/test_0430_browse_utilities.py
M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
M test/tool_shed/functional/test_0450_skip_tool_tests.py
M test/tool_shed/functional/test_0460_upload_to_repository.py
M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
M test/tool_shed/functional/test_0490_export_import_repositories.py
M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
M test/tool_shed/functional/test_0530_repository_admin_feature.py
M test/tool_shed/functional/test_1000_install_basic_repository.py
M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_1060_install_repository_with_workflow.py
M test/tool_shed/functional/test_1070_invalid_tool.py
M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
M test/tool_shed/functional/test_1085_repository_dependency_handling.py
M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py
M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py
M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py
M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_1130_datatype_converters.py
M test/tool_shed/functional/test_1140_tool_help_images.py
M test/tool_shed/functional/test_1150_prior_installation_required.py
M test/tool_shed/functional/test_1160_circular_prior_installation_required.py
M test/tool_shed/functional/test_1170_complex_prior_installation_required.py
M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1300_reset_all_metadata.py
M test/tool_shed/functional/test_1400_review_migration_stages.py
M test/tool_shed/functional/test_1410_update_manager.py
M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
M test/tool_shed/functional/test_1430_repair_installed_repository.py
M test/tool_shed/functional/test_1440_missing_env_sh_files.py
M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
M test/tool_shed/functional/test_1460_data_managers.py
M test/tool_shed/functional/test_1470_updating_installed_repositories.py
M test/tool_shed/functional_tests.py
M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_rules/20_instance.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_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_objectstore.py
M test/unit/test_routes.py
M test/unit/test_sockets.py
M test/unit/tool_shed_unit_tests/test_fabric_util.py
M test/unit/tool_shed_unit_tests/test_td_common_util.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox_filters.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/workflows/test_extract_summary.py
M test/unit/workflows/test_modules.py
M tool-data/all_fasta.loc.sample
M tool-data/faseq.loc.sample
R tool-data/fastx_clipper_sequences.txt
M tool-data/liftOver.loc.sample
M tool-data/mosaik_index.loc.sample
M tool-data/ngs_sim_fasta.loc.sample
M tool-data/perm_base_index.loc.sample
M tool-data/perm_color_index.loc.sample
M tool-data/picard_index.loc.sample
M tool-data/regions.loc.sample
R tool-data/shared/ucsc/manual_builds.txt
A tool-data/shared/ucsc/manual_builds.txt.sample
M tool-data/srma_index.loc.sample
M tool_list.py
M tools/data_source/biomart.xml
M tools/data_source/biomart_test.xml
M tools/data_source/data_source.py
R tools/data_source/echo.py
R tools/data_source/echo.xml
R tools/data_source/ucsc_archaea.xml
R tools/data_source/ucsc_filter.py
R tools/data_source/ucsc_proxy.py
R tools/data_source/ucsc_proxy.xml
M tools/data_source/ucsc_tablebrowser.xml
M tools/data_source/ucsc_tablebrowser_archaea.xml
M tools/data_source/ucsc_tablebrowser_test.xml
R tools/data_source/ucsc_testproxy.xml
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/cutWrapper.xml
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_file_browser_dev.xml
M tools/genomespace/genomespace_file_browser_prod.xml
M tools/genomespace/genomespace_file_browser_test.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/sr_mapping/bfast_wrapper.xml
M tools/sr_mapping/fastq_statistics.xml
M tools/sr_mapping/mosaik.xml
M tools/sr_mapping/srma_wrapper.xml
M tools/stats/grouping.py
M tools/visualization/LAJ.xml
M tox.ini
Log Message:
-----------
(merge dev)
Commit: 5dfb3ffbecf18c9bc1275a4aae7024f69e5ef303
https://github.com/galaxyproject/galaxy/commit/5dfb3ffbecf18c9bc1275a4aae70…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-10-27 (Tue, 27 Oct 2015)
Changed paths:
A client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/apps/galaxy.js
M client/galaxy/scripts/apps/history-app.js
M client/galaxy/scripts/galaxy-app-base.js
M client/galaxy/scripts/galaxy.base.js
M client/galaxy/scripts/libs/common-libs.js
M client/galaxy/scripts/mvc/app/app-analysis.js
M client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/webpack.config.js
M lib/galaxy/web/base/controller.py
M static/maps/apps/history-app.js.map
M static/maps/galaxy-app-base.js.map
M static/maps/libs/common-libs.js.map
M static/maps/mvc/app/app-analysis.js.map
M static/maps/mvc/app/app-view.js.map
M static/maps/mvc/base-mvc.js.map
M static/maps/mvc/tools.js.map
M static/maps/mvc/user/user-model.js.map
M static/scripts/apps/history-app.js
R static/scripts/bundled/common.js
R static/scripts/bundled/history.bundled.js
R static/scripts/bundled/libs.bundled.js
M static/scripts/galaxy-app-base.js
M static/scripts/libs/common-libs.js
M static/scripts/mvc/app/app-view.js
M static/scripts/mvc/base-mvc.js
M static/scripts/mvc/tools.js
M static/scripts/mvc/user/user-model.js
M static/scripts/templates/compiled/tool_form.js
M templates/base.mako
M templates/base/base_panels.mako
M templates/galaxy_client_app.mako
M templates/js-app.mako
M templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Webpack: test index page (Analyze Data) working, original working, history app working
Commit: cebfdd2745b4695f7d61e6d5b95984dee0f3eba6
https://github.com/galaxyproject/galaxy/commit/cebfdd2745b4695f7d61e6d5b959…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-10-27 (Tue, 27 Oct 2015)
Changed paths:
M client/grunt-tasks/scripts.js
M static/maps/libs/common-libs.js.map
M static/maps/mvc/tools.js.map
M static/scripts/libs/common-libs.js
M static/scripts/mvc/tools.js
M static/scripts/templates/compiled/tool_form.js
Log Message:
-----------
Webpack: restore original page scripts
Commit: 7bfbb71b27af3147a18beaf2fdd889c7e1c7455d
https://github.com/galaxyproject/galaxy/commit/7bfbb71b27af3147a18beaf2fdd8…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-10-27 (Tue, 27 Oct 2015)
Changed paths:
M .gitignore
A lib/galaxy/webapps/galaxy/controllers/test.py
Log Message:
-----------
Webpack: temp add test controller, add bundled webpack directory to gitignore
Commit: 2513e766be2ac2a37b87ff7682dff83688bed815
https://github.com/galaxyproject/galaxy/commit/2513e766be2ac2a37b87ff7682df…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-10-28 (Wed, 28 Oct 2015)
Changed paths:
A static/scripts/bundled/analysis.bundled.js
A static/scripts/bundled/analysis.bundled.js.map
A static/scripts/bundled/common.js
A static/scripts/bundled/common.js.map
A static/scripts/bundled/galaxy.bundled.js
A static/scripts/bundled/galaxy.bundled.js.map
A static/scripts/bundled/history.bundled.js
A static/scripts/bundled/history.bundled.js.map
A static/scripts/bundled/libs.bundled.js
A static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Webpack: adding production bundles
Commit: 4ce8b3d96a0922483de24afe8c02e221ef142f57
https://github.com/galaxyproject/galaxy/commit/4ce8b3d96a0922483de24afe8c02…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-10-28 (Wed, 28 Oct 2015)
Changed paths:
M lib/galaxy/managers/users.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/test.py
M templates/js-app.mako
Log Message:
-----------
Managers, users: change serialize_current_anonymous_user to return None when no history present; Webpack: move jsAppLauncher test controller into root controller, replace index method
Commit: 790c2f5954fbb30ad4c3c0362bbd01ab85de9e3a
https://github.com/galaxyproject/galaxy/commit/790c2f5954fbb30ad4c3c0362bbd…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-10-28 (Wed, 28 Oct 2015)
Changed paths:
R lib/galaxy/webapps/galaxy/controllers/test.py
Log Message:
-----------
Webpack: remove test controller
Commit: 1b89d839aed4c14c5cf62e4b6f3c9b4816f419d2
https://github.com/galaxyproject/galaxy/commit/1b89d839aed4c14c5cf62e4b6f3c…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-10-28 (Wed, 28 Oct 2015)
Changed paths:
M templates/base/base_panels.mako
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Webpack: fix newlibs jquery
Commit: 9a659d85d6896dffa280005e66cc72abc0dcbab1
https://github.com/galaxyproject/galaxy/commit/9a659d85d6896dffa280005e66cc…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-03 (Tue, 03 Nov 2015)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/common.js
M static/scripts/bundled/common.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/bundled/history.bundled.js
M static/scripts/bundled/history.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
M templates/base.mako
M templates/base/base_panels.mako
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Webpack: use bundled libs in base templates
Commit: 84b40650ec1adc98879457fe087c5d802838b421
https://github.com/galaxyproject/galaxy/commit/84b40650ec1adc98879457fe087c…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-03 (Tue, 03 Nov 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
M .gitignore
M client/galaxy/scripts/galaxy-app-base.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/mvc/app/app-analysis.js
A client/galaxy/scripts/mvc/app/app-login.js
M client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/citation/citation-model.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-panel.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/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/dataset/dataset-list.js
M client/galaxy/scripts/mvc/dataset/dataset-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
M client/galaxy/scripts/mvc/history/history-panel.js
M client/galaxy/scripts/mvc/history/history-structure-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/job/job-model.js
M client/galaxy/scripts/mvc/list/list-item.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/mvc/tags.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/templates/compiled/tool_link.js
M client/galaxy/scripts/templates/tool_link.handlebars
M client/galaxy/scripts/utils/add-logging.js
M client/galaxy/scripts/utils/deferred.js
M client/galaxy/scripts/utils/metrics-logger.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/bootstrap.less
M config/plugins/visualizations/charts/static/build-app.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/tools.js
M config/plugins/visualizations/charts/static/views/group.js
M config/plugins/visualizations/charts/static/views/viewport.js
M doc/source/lib/galaxy.auth.providers.rst
M doc/source/lib/galaxy.datatypes.rst
A doc/source/lib/galaxy.dependencies.rst
M doc/source/lib/galaxy.eggs.rst
M doc/source/lib/galaxy.jobs.runners.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.tools.deps.resolvers.rst
M doc/source/lib/galaxy.web.framework.middleware.rst
M doc/source/lib/galaxy.webapps.galaxy.controllers.rst
M doc/source/lib/galaxy.webapps.reports.controllers.rst
M doc/source/lib/galaxy.webapps.rst
M doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/lib/modules.rst
R doc/source/lib/pkg_resources.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/runners/drmaa.py
A lib/galaxy/jobs/runners/util/drmaa/__init__.py
A lib/galaxy/jobs/runners/util/retry.py
A lib/galaxy/jobs/runners/util/sudo.py
M lib/galaxy/main.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/dockerfiles.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/lint.py
A lib/galaxy/tools/lint_util.py
M lib/galaxy/tools/linters/command.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/linters/outputs.py
A lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/linters/top_level.py
A lib/galaxy/tools/linters/xml_order.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/pulsar/client/transport/curl.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/hg_util.py
M run.sh
M run_tests.sh
A scripts/binary_compatibility.py
M scripts/common_startup.sh
A scripts/galaxy-main
M scripts/tools/maf/check_loc_file.py
M static/maps/galaxy-app-base.js.map
M static/maps/galaxy.library.js.map
M static/maps/mvc/app/app-analysis.js.map
A static/maps/mvc/app/app-login.js.map
M static/maps/mvc/app/app-view.js.map
M static/maps/mvc/base-mvc.js.map
M static/maps/mvc/citation/citation-model.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-panel.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/dataset/dataset-choice.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/dataset/dataset-list.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/history/history-content-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-panel.js.map
M static/maps/mvc/history/history-structure-view.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/job/job-model.js.map
M static/maps/mvc/list/list-item.js.map
M static/maps/mvc/list/list-panel.js.map
M static/maps/mvc/tags.js.map
M static/maps/mvc/tools.js.map
M static/maps/mvc/tools/tools-form-base.js.map
M static/maps/mvc/user/user-model.js.map
M static/maps/mvc/user/user-quotameter.js.map
M static/maps/mvc/visualization/visualization-model.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/maps/templates/compiled/tool_link.js.map
M static/maps/utils/add-logging.js.map
M static/maps/utils/deferred.js.map
M static/maps/utils/metrics-logger.js.map
M static/scripts/galaxy-app-base.js
M static/scripts/galaxy.library.js
M static/scripts/mvc/app/app-analysis.js
A static/scripts/mvc/app/app-login.js
M static/scripts/mvc/app/app-view.js
M static/scripts/mvc/base-mvc.js
M static/scripts/mvc/citation/citation-model.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-panel.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/dataset/dataset-list.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/history/history-structure-view.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/tools.js
M static/scripts/mvc/tools/tools-form-base.js
M static/scripts/mvc/user/user-model.js
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/templates/compiled/tool_link.js
M static/scripts/utils/add-logging.js
M static/scripts/utils/deferred.js
M static/scripts/utils/metrics-logger.js
M static/style/blue/base.css
M static/welcome.html.sample
M test/qunit/tests/galaxy-app-base.js
M tools/data_source/data_source.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/catWrapper.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/sort_gtf.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/lav_to_bed.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/maf/interval2maf.py
M tools/maf/interval2maf.xml
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/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/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
(merge dev)
Commit: d80d74c8880c8194dc2c727b7fc9dbf2297483f0
https://github.com/galaxyproject/galaxy/commit/d80d74c8880c8194dc2c727b7fc9…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-05 (Thu, 05 Nov 2015)
Changed paths:
M client/galaxy/scripts/galaxy-app-base.js
M client/galaxy/scripts/galaxy.base.js
M client/galaxy/scripts/galaxy.panels.js
A client/galaxy/scripts/libs/backbone.js
R client/galaxy/scripts/libs/backbone/backbone.js
M client/galaxy/scripts/libs/common-libs.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/grunt-tasks/install-libs.js
M client/webpack.config.js
M static/maps/galaxy-app-base.js.map
M static/maps/galaxy.panels.js.map
A static/maps/libs/backbone.js.map
M static/maps/libs/common-libs.js.map
M static/maps/mvc/base-mvc.js.map
M static/maps/mvc/user/user-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
R static/scripts/bundled/common.js
R static/scripts/bundled/common.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
R static/scripts/bundled/history.bundled.js
R static/scripts/bundled/history.bundled.js.map
R static/scripts/bundled/libs.bundled.js
R static/scripts/bundled/libs.bundled.js.map
M static/scripts/galaxy-app-base.js
M static/scripts/galaxy.base.js
M static/scripts/galaxy.panels.js
A static/scripts/libs/backbone.js
M static/scripts/libs/common-libs.js
M static/scripts/mvc/base-mvc.js
M static/scripts/mvc/user/user-model.js
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
M templates/webapps/galaxy/dataset/display.mako
M templates/webapps/galaxy/dataset/tabular_chunked.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/visualization/display.mako
M templates/webapps/galaxy/visualization/sweepster.mako
Log Message:
-----------
Client libs: move backbone down into /libs (not backbone/backbone); Webpack: move to non-entry vendor bundling for libraries, clean up assoc.
Commit: 4f242151e7f6519e27ecae04632bdbbccddb2879
https://github.com/galaxyproject/galaxy/commit/4f242151e7f6519e27ecae04632b…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-05 (Thu, 05 Nov 2015)
Changed paths:
R client/galaxy/scripts/apps/history-app.js
R client/galaxy/scripts/apps/libs.js
R client/galaxy/scripts/libs/common-libs.js
R static/maps/apps/history-app.js.map
R static/maps/apps/libs.js.map
M static/maps/galaxy-app-base.js.map
M static/maps/galaxy.base.js.map
R static/scripts/apps/history-app.js
R static/scripts/apps/libs.js
M static/scripts/galaxy-app-base.js
M static/scripts/galaxy.base.js
M static/scripts/mvc/base-mvc.js
Log Message:
-----------
Webpack: remove libs and history apps, grunt:pack scripts
Commit: e59d08f85631eacb83eada88c3351e4c19bcd667
https://github.com/galaxyproject/galaxy/commit/e59d08f85631eacb83eada88c335…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-06 (Fri, 06 Nov 2015)
Changed paths:
R client/galaxy/scripts/galaxy-app-webpack.js
A client/galaxy/scripts/galaxy-async.js
R client/galaxy/scripts/galaxy.autocom_tagging.js
M client/galaxy/scripts/galaxy.base.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/galaxy.panels.js
A client/galaxy/scripts/modal.js
M client/galaxy/scripts/mvc/annotations.js
M client/galaxy/scripts/mvc/app/app-analysis.js
M client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/scripts/mvc/collection/collection-panel-edit.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/history-panel-edit.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
A client/galaxy/scripts/polyfills.js
A client/galaxy/scripts/ui/autocom_tagging.js
A client/galaxy/scripts/ui/editable-text.js
A client/galaxy/scripts/ui/popupmenu.js
A client/galaxy/scripts/utils/async-save-text.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/trackster/util.js
M client/webpack.config.js
R static/maps/galaxy-app-webpack.js.map
A static/maps/galaxy-async.js.map
R static/maps/galaxy.autocom_tagging.js.map
M static/maps/galaxy.base.js.map
M static/maps/galaxy.pages.js.map
M static/maps/galaxy.panels.js.map
A static/maps/modal.js.map
M static/maps/mvc/annotations.js.map
M static/maps/mvc/app/app-analysis.js.map
M static/maps/mvc/app/app-view.js.map
M static/maps/mvc/collection/collection-panel-edit.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/history-panel-edit.js.map
M static/maps/mvc/workflow/workflow-view.js.map
A static/maps/polyfills.js.map
A static/maps/ui/autocom_tagging.js.map
A static/maps/ui/editable-text.js.map
A static/maps/ui/popupmenu.js.map
A static/maps/utils/async-save-text.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/trackster/util.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
R static/scripts/galaxy-app-webpack.js
A static/scripts/galaxy-async.js
R static/scripts/galaxy.autocom_tagging.js
M static/scripts/galaxy.base.js
M static/scripts/galaxy.pages.js
M static/scripts/galaxy.panels.js
A static/scripts/modal.js
M static/scripts/mvc/annotations.js
M static/scripts/mvc/app/app-view.js
M static/scripts/mvc/collection/collection-panel-edit.js
M static/scripts/mvc/history/history-panel-edit.js
M static/scripts/mvc/workflow/workflow-view.js
A static/scripts/polyfills.js
A static/scripts/ui/autocom_tagging.js
A static/scripts/ui/editable-text.js
A static/scripts/ui/popupmenu.js
A static/scripts/utils/async-save-text.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/tracks.js
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
M templates/refresh_frames.mako
M templates/tagging_common.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Webpack: move vendor to libs; break up galaxy.panels to panels and modal; break up galaxy.base to polyfills, galaxy-async, ui/popupmenu, ui/editable-text, and utils/async-save-text; move reset_tool_search into workflow-view; move commatize into trackster/util; move galaxy.autocom_tagging to ui/autocom_tagging
Commit: 9c35d35c52eca6638e25459293ac9a28e40f9d63
https://github.com/galaxyproject/galaxy/commit/9c35d35c52eca6638e25459293ac…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-09 (Mon, 09 Nov 2015)
Changed paths:
R client/galaxy/scripts/galaxy.base.js
M client/galaxy/scripts/galaxy.masthead.js
R client/galaxy/scripts/galaxy.panels.js
M client/galaxy/scripts/mvc/app/app-view.js
A client/galaxy/scripts/onload.js
A client/galaxy/scripts/panel.js
M client/galaxy/scripts/ui/autocom_tagging.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/trackster/util.js
M client/webpack.config.js
R static/maps/galaxy.base.js.map
R static/maps/galaxy.panels.js.map
M static/maps/mvc/app/app-view.js.map
A static/maps/onload.js.map
A static/maps/panel.js.map
M static/maps/ui/autocom_tagging.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/trackster/util.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
R static/scripts/galaxy.base.js
R static/scripts/galaxy.panels.js
M static/scripts/mvc/app/app-view.js
A static/scripts/onload.js
A static/scripts/panel.js
M static/scripts/ui/autocom_tagging.js
M static/scripts/viz/trackster/util.js
Log Message:
-----------
Webpack: make autocom_tagging into a module, export commatize, rename galaxy.base to onload and galaxy.panels to panels
Commit: 649a83c1aa8026160f8d77cb423547ecb76cda28
https://github.com/galaxyproject/galaxy/commit/649a83c1aa8026160f8d77cb4235…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-09 (Mon, 09 Nov 2015)
Changed paths:
M client/galaxy/scripts/galaxy.frame.js
M client/galaxy/scripts/galaxy.masthead.js
M client/galaxy/scripts/galaxy.menu.js
M client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/style/less/base.less
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M static/maps/galaxy.frame.js.map
M static/maps/galaxy.masthead.js.map
M static/maps/galaxy.menu.js.map
M static/maps/mvc/app/app-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/galaxy.frame.js
M static/scripts/galaxy.masthead.js
M static/scripts/galaxy.menu.js
M static/scripts/mvc/app/app-view.js
M static/style/blue/base.css
M templates/js-app.mako
M templates/webapps/galaxy/galaxy.masthead.mako
Log Message:
-----------
Webpack: (shoulda been 2 sep. commits) re-add minimal DOM for 1,2,3 panel layouts via server-side/js-app.mako, correct noscript tag styling; Instantiate galaxy.frame and galaxy.menu from galaxy.masthead (currently the only user), reverse dependencies in them (masthead imports them), and move GalaxyMastheadTab into galaxy.menu and GalaxyMastheadIcon into galaxy.frame - allowing a single import of galaxy.masthead
Commit: a639b0c996b13d45412115009615af826ca38ed8
https://github.com/galaxyproject/galaxy/commit/a639b0c996b13d45412115009615…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-09 (Mon, 09 Nov 2015)
Changed paths:
R client/galaxy/scripts/galaxy.frame.js
R client/galaxy/scripts/galaxy.masthead.js
R client/galaxy/scripts/galaxy.menu.js
A client/galaxy/scripts/layout/masthead.js
A client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/layout/panel.js
A client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/app/app-view.js
R client/galaxy/scripts/panel.js
M client/webpack.config.js
R static/maps/galaxy.frame.js.map
R static/maps/galaxy.masthead.js.map
R static/maps/galaxy.menu.js.map
A static/maps/layout/masthead.js.map
A static/maps/layout/menu.js.map
A static/maps/layout/panel.js.map
A static/maps/layout/scratchbook.js.map
M static/maps/mvc/app/app-view.js.map
R static/maps/panel.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
R static/scripts/galaxy.frame.js
R static/scripts/galaxy.masthead.js
R static/scripts/galaxy.menu.js
A static/scripts/layout/masthead.js
A static/scripts/layout/menu.js
A static/scripts/layout/panel.js
A static/scripts/layout/scratchbook.js
M static/scripts/mvc/app/app-view.js
R static/scripts/panel.js
M templates/webapps/galaxy/galaxy.masthead.mako
Log Message:
-----------
Webpack: move galaxy.masthead and galaxy.menu to layout/masthead and layout/menu, panel to layout/panel, and rename galaxy.frame to layout/scratchbook
Commit: b1266b45dc4ddd63a2b2ae1cc9c28ba9d43a2bc0
https://github.com/galaxyproject/galaxy/commit/b1266b45dc4ddd63a2b2ae1cc9c2…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-11 (Wed, 11 Nov 2015)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/galaxy.js
A client/galaxy/scripts/apps/history-panel.js
A client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/galaxy-app-base.js
A client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/onload.js
M client/webpack.config.js
M lib/galaxy/webapps/galaxy/controllers/root.py
M static/maps/galaxy-app-base.js.map
A static/maps/layout/page.js.map
M static/maps/layout/panel.js.map
M static/maps/mvc/tools.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/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/galaxy-app-base.js
A static/scripts/layout/page.js
M static/scripts/layout/panel.js
M static/scripts/mvc/tools.js
M static/scripts/onload.js
M templates/base/base_panels.mako
M templates/js-app.mako
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Webpack: move panel to Backbone, implement ToolPanel and HistoryPanel; simplify js-app.mako (by removing alternate layouts); clean up debugging info, make Galaxy less chatty before logging setup
Commit: c1cc3bd483fc2197b43048f467be6e80f80babea
https://github.com/galaxyproject/galaxy/commit/c1cc3bd483fc2197b43048f467be…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/mvc/library/library-folderlist-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/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/galaxy.library.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M templates/base/base_panels.mako
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Webpack: fix masthead in libraries; update Panel usage in base_panels.mako, galaxy.panels.mako
Commit: a4edf159be9996d09bb029d2098d9c0d39fb2975
https://github.com/galaxyproject/galaxy/commit/a4edf159be9996d09bb029d2098d…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
M .gitignore
M CONTRIBUTORS.md
M client/galaxy/scripts/galaxy-app-base.js
M client/galaxy/scripts/libs/jquery/select2.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.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-select-content.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M client/galaxy/scripts/mvc/tools/tools-form-workflow.js
M client/galaxy/scripts/mvc/tools/tools-jobs.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/utils/deferred.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M config/plugins/visualizations/charts/static/build-app.js
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M run.sh
A scripts/check_eggs.py
A scripts/fetch_eggs.py
M static/maps/galaxy-app-base.js.map
M static/maps/libs/jquery/select2.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/tools/tools-form-base.js.map
M static/maps/mvc/tools/tools-form-workflow.js.map
M static/maps/mvc/tools/tools-jobs.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/utils/deferred.js.map
M static/maps/utils/uploadbox.js.map
M static/scripts/galaxy-app-base.js
M static/scripts/libs/jquery/select2.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/tools/tools-form-base.js
M static/scripts/mvc/tools/tools-form-workflow.js
M static/scripts/mvc/tools/tools-jobs.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/utils/deferred.js
M static/scripts/utils/uploadbox.js
M static/style/blue/base.css
M test/api/helpers.py
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/unicode_stream.xml
M test/unit/jobs/test_job_output_checker.py
M tools/filters/wig_to_bigwig.xml
M tools/stats/gsummary.py
Log Message:
-----------
(merge dev)
Commit: dc0b960ea1242ae3ec34e7d00c5f8619e06f7b59
https://github.com/galaxyproject/galaxy/commit/dc0b960ea1242ae3ec34e7d00c5f…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/onload.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
M static/scripts/onload.js
M templates/base/base_panels.mako
M templates/js-app.mako
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Webpack: lowercase DD-helper throughout project to reflect changes in 7717659
Commit: 78e6253178b51afa77346b259801f221eb9c201e
https://github.com/galaxyproject/galaxy/commit/78e6253178b51afa77346b259801…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
A client/galaxy/scripts/layout/modal.js
R client/galaxy/scripts/modal.js
M client/galaxy/scripts/onload.js
M client/webpack.config.js
A static/maps/layout/modal.js.map
R static/maps/modal.js.map
A static/scripts/layout/modal.js
R static/scripts/modal.js
Log Message:
-----------
Webpack: move old school modal into layout/
Commit: 215391f571f72725a87f45b556be10e8446db8a9
https://github.com/galaxyproject/galaxy/commit/215391f571f72725a87f45b556be…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
R client/galaxy/scripts/galaxy-async.js
R static/maps/galaxy-async.js.map
R static/scripts/galaxy-async.js
Log Message:
-----------
Webpack: remove galaxy-async
Commit: 350a53f1ef9c686ad3617cc37f037251a79a28ef
https://github.com/galaxyproject/galaxy/commit/350a53f1ef9c686ad3617cc37f03…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
R client/galaxy/scripts/base.js
M client/galaxy/scripts/viz/trackster.js
R static/maps/base.js.map
M static/maps/viz/trackster.js.map
R static/scripts/base.js
M static/scripts/viz/trackster.js
Log Message:
-----------
Webpack: move base.Base to trackster (which uses it)
Commit: f971e17f95d62662eaec47a96da88f1b45d823ce
https://github.com/galaxyproject/galaxy/commit/f971e17f95d62662eaec47a96da8…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
R client/galaxy/scripts/galaxy.ui.scrollPanel.js
A client/galaxy/scripts/ui/scroll-panel.js
R static/maps/galaxy.ui.scrollPanel.js.map
A static/maps/ui/scroll-panel.js.map
R static/scripts/galaxy.ui.scrollPanel.js
A static/scripts/ui/scroll-panel.js
Log Message:
-----------
Webpack: move galaxy.ui.scrollPanel into ui/scroll-panel
Commit: 93629bb29e35340618aca2d1b420d948b56c695b
https://github.com/galaxyproject/galaxy/commit/93629bb29e35340618aca2d1b420…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
M client/galaxy/scripts/mvc/tools.js
M client/package.json
M client/webpack.config.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
Log Message:
-----------
Webpack: add handlebars loader, update tools.js
Commit: 2f0b64613770c8e59613bb46218e12565d260038
https://github.com/galaxyproject/galaxy/commit/2f0b64613770c8e59613bb46218e…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/galaxy.tools.js
M client/galaxy/scripts/mvc/app/app-analysis.js
R client/galaxy/scripts/mvc/tools.js
A client/galaxy/scripts/mvc/tools/tools.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster/tracks.js
R static/maps/mvc/tools.js.map
A static/maps/mvc/tools/tools.js.map
R static/scripts/mvc/tools.js
A static/scripts/mvc/tools/tools.js
Log Message:
-----------
Webpack: move tools.js into mvc/tools/
Commit: 372c2e9e43854b0e5e576abcead50e22f00923d9
https://github.com/galaxyproject/galaxy/commit/372c2e9e43854b0e5e576abcead5…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
M client/galaxy/scripts/layout/scratchbook.js
R client/galaxy/scripts/mvc/data.js
A client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/tools/tools.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M static/maps/galaxy.tools.js.map
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/app/app-analysis.js.map
R static/maps/mvc/data.js.map
A static/maps/mvc/dataset/data.js.map
M static/maps/mvc/tools/tools.js.map
M static/maps/onload.js.map
M static/maps/ui/scroll-panel.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/sweepster.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/visualization.js.map
M static/scripts/galaxy.tools.js
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/app/app-analysis.js
R static/scripts/mvc/data.js
A static/scripts/mvc/dataset/data.js
M static/scripts/mvc/tools/tools.js
M static/scripts/onload.js
M static/scripts/ui/scroll-panel.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M templates/webapps/galaxy/dataset/display.mako
M templates/webapps/galaxy/dataset/tabular_chunked.mako
Log Message:
-----------
Webpack: move data.js into dataset/data.js; pack scripts
Commit: 6d0ab669ecbd12e75cf38f8c914bbf5954caac20
https://github.com/galaxyproject/galaxy/commit/6d0ab669ecbd12e75cf38f8c914b…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/webpack.config.js
M static/maps/mvc/citation/citation-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/mvc/citation/citation-model.js
Log Message:
-----------
Webpack: correctly load jQuery-ui, require bibtex in citations, and move polyfills to first loaded
Commit: c66bc7ab766e2af197a668a76e15e1dc21cfb9fa
https://github.com/galaxyproject/galaxy/commit/c66bc7ab766e2af197a668a76e15…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
R client/galaxy/scripts/mvc/collection/collection-panel-edit.js
R client/galaxy/scripts/mvc/collection/collection-panel.js
A client/galaxy/scripts/mvc/collection/collection-view-edit.js
A client/galaxy/scripts/mvc/collection/collection-view.js
R client/galaxy/scripts/mvc/history/history-panel-annotated.js
R client/galaxy/scripts/mvc/history/history-panel-edit-current.js
R client/galaxy/scripts/mvc/history/history-panel-edit.js
R client/galaxy/scripts/mvc/history/history-panel.js
A client/galaxy/scripts/mvc/history/history-view-annotated.js
A client/galaxy/scripts/mvc/history/history-view-edit-current.js
A client/galaxy/scripts/mvc/history/history-view-edit.js
A client/galaxy/scripts/mvc/history/history-view.js
M client/webpack.config.js
R static/maps/mvc/collection/collection-panel-edit.js.map
R static/maps/mvc/collection/collection-panel.js.map
A static/maps/mvc/collection/collection-view-edit.js.map
A static/maps/mvc/collection/collection-view.js.map
R static/maps/mvc/history/history-panel-annotated.js.map
R static/maps/mvc/history/history-panel-edit-current.js.map
R static/maps/mvc/history/history-panel-edit.js.map
R static/maps/mvc/history/history-panel.js.map
A static/maps/mvc/history/history-view-annotated.js.map
A static/maps/mvc/history/history-view-edit-current.js.map
A static/maps/mvc/history/history-view-edit.js.map
A static/maps/mvc/history/history-view.js.map
R static/scripts/mvc/collection/collection-panel-edit.js
R static/scripts/mvc/collection/collection-panel.js
A static/scripts/mvc/collection/collection-view-edit.js
A static/scripts/mvc/collection/collection-view.js
R static/scripts/mvc/history/history-panel-annotated.js
R static/scripts/mvc/history/history-panel-edit-current.js
R static/scripts/mvc/history/history-panel-edit.js
R static/scripts/mvc/history/history-panel.js
A static/scripts/mvc/history/history-view-annotated.js
A static/scripts/mvc/history/history-view-edit-current.js
A static/scripts/mvc/history/history-view-edit.js
A static/scripts/mvc/history/history-view.js
Log Message:
-----------
Webpack: normalize history and panel module names with other mvc modules (history-panel is not a panel - just a view)
Commit: 55068dea285c82232bd9dbf024de580013c5f3d8
https://github.com/galaxyproject/galaxy/commit/55068dea285c82232bd9dbf024de…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-12 (Thu, 12 Nov 2015)
Changed paths:
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/mvc/app/app-analysis.js
M client/galaxy/scripts/mvc/base-mvc.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/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.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/list/list-panel.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M static/maps/mvc/app/app-analysis.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/history-view-annotated.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/mvc/app/app-analysis.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/multi-panel.js
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/history/view_multiple.mako
Log Message:
-----------
Webpack: normalize 'panel' names part-2: history and collection modules
Commit: 8efabbbcd5546441182cbff1cc66e525cf6abf48
https://github.com/galaxyproject/galaxy/commit/8efabbbcd5546441182cbff1cc66…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-13 (Fri, 13 Nov 2015)
Changed paths:
M templates/grid_base.mako
M templates/webapps/galaxy/dataset/edit_attributes.mako
M templates/webapps/galaxy/library/common/ldda_edit_info.mako
M templates/webapps/galaxy/library/common/move_library_item.mako
M templates/webapps/galaxy/library/common/upload.mako
M templates/webapps/galaxy/page/editor.mako
M templates/webapps/galaxy/requests/common/create_request.mako
M templates/webapps/galaxy/requests/common/find_samples.mako
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Webpack: fix load order in embedded grids by removing autocom_tagging script tag (it's in the libs.bundle), remove it from other mako templates as well; remove bibtex script from workflow/editor.mako (unused)
Commit: c3f4b54b686ba93b3bb8f65d17f3961d344b9d7c
https://github.com/galaxyproject/galaxy/commit/c3f4b54b686ba93b3bb8f65d17f3…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-13 (Fri, 13 Nov 2015)
Changed paths:
M client/galaxy/scripts/galaxy-app-base.js
M client/galaxy/scripts/utils/localization.js
R client/galaxy/scripts/utils/webpack-localization.js
M client/package.json
M client/webpack.config.js
M static/maps/galaxy-app-base.js.map
M static/maps/utils/localization.js.map
R static/maps/utils/webpack-localization.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/utils/localization.js
R static/scripts/utils/webpack-localization.js
Log Message:
-----------
Webpack, localization: support both requirejs and webpack i18n by including the amdi18n-loader (both now share the utils/localization file)
Commit: 6f754216a4100969b18185aa705065b03a215628
https://github.com/galaxyproject/galaxy/commit/6f754216a4100969b18185aa7050…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-13 (Fri, 13 Nov 2015)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/dataset-list.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
R client/galaxy/scripts/mvc/list/list-panel.js
A client/galaxy/scripts/mvc/list/list-view.js
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/dataset/dataset-list.js.map
M static/maps/mvc/history/history-view.js.map
R static/maps/mvc/list/list-panel.js.map
A static/maps/mvc/list/list-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/dataset-list.js
M static/scripts/mvc/history/history-view.js
R static/scripts/mvc/list/list-panel.js
A static/scripts/mvc/list/list-view.js
Log Message:
-----------
Webpack: normalize list-panel to list-view
Commit: d285c01108f59d1b054955f312b16c3b978aa97a
https://github.com/galaxyproject/galaxy/commit/d285c01108f59d1b054955f312b1…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-13 (Fri, 13 Nov 2015)
Changed paths:
A client/galaxy/scripts/mvc/annotation.js
R client/galaxy/scripts/mvc/annotations.js
A client/galaxy/scripts/mvc/tag.js
R client/galaxy/scripts/mvc/tags.js
A client/galaxy/scripts/mvc/tool/tools-form-base.js
A client/galaxy/scripts/mvc/tool/tools-form-workflow.js
A client/galaxy/scripts/mvc/tool/tools-form.js
A client/galaxy/scripts/mvc/tool/tools-jobs.js
A client/galaxy/scripts/mvc/tool/tools-template.js
A client/galaxy/scripts/mvc/tool/tools.js
R client/galaxy/scripts/mvc/tools/tools-form-base.js
R client/galaxy/scripts/mvc/tools/tools-form-workflow.js
R client/galaxy/scripts/mvc/tools/tools-form.js
R client/galaxy/scripts/mvc/tools/tools-jobs.js
R client/galaxy/scripts/mvc/tools/tools-template.js
R client/galaxy/scripts/mvc/tools/tools.js
Log Message:
-----------
Webpack: normalize tags, annotations, and tools (the names of)
Commit: 894af4c5deadc75d2f1a5e11e26abc9c3f4f7256
https://github.com/galaxyproject/galaxy/commit/894af4c5deadc75d2f1a5e11e26a…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-13 (Fri, 13 Nov 2015)
Changed paths:
A static/maps/mvc/annotation.js.map
R static/maps/mvc/annotations.js.map
A static/maps/mvc/tag.js.map
R static/maps/mvc/tags.js.map
A static/maps/mvc/tool/tools-form-base.js.map
A static/maps/mvc/tool/tools-form-workflow.js.map
A static/maps/mvc/tool/tools-form.js.map
A static/maps/mvc/tool/tools-jobs.js.map
A static/maps/mvc/tool/tools-template.js.map
A static/maps/mvc/tool/tools.js.map
R static/maps/mvc/tools/tools-form-base.js.map
R static/maps/mvc/tools/tools-form-workflow.js.map
R static/maps/mvc/tools/tools-form.js.map
R static/maps/mvc/tools/tools-jobs.js.map
R static/maps/mvc/tools/tools-template.js.map
R static/maps/mvc/tools/tools.js.map
A static/scripts/mvc/annotation.js
R static/scripts/mvc/annotations.js
A static/scripts/mvc/tag.js
R static/scripts/mvc/tags.js
A static/scripts/mvc/tool/tools-form-base.js
A static/scripts/mvc/tool/tools-form-workflow.js
A static/scripts/mvc/tool/tools-form.js
A static/scripts/mvc/tool/tools-jobs.js
A static/scripts/mvc/tool/tools-template.js
A static/scripts/mvc/tool/tools.js
R static/scripts/mvc/tools/tools-form-base.js
R static/scripts/mvc/tools/tools-form-workflow.js
R static/scripts/mvc/tools/tools-form.js
R static/scripts/mvc/tools/tools-jobs.js
R static/scripts/mvc/tools/tools-template.js
R static/scripts/mvc/tools/tools.js
Log Message:
-----------
Webpack: normalize tags, annotations, and tools (2 of 3)
Commit: cc6c15f3b102afd22c3a9f1c7d1a5d92daad03bc
https://github.com/galaxyproject/galaxy/commit/cc6c15f3b102afd22c3a9f1c7d1a…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-13 (Fri, 13 Nov 2015)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/mvc/app/app-analysis.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/tool/tools-form-base.js
M client/galaxy/scripts/mvc/tool/tools-form-workflow.js
M client/galaxy/scripts/mvc/tool/tools-form.js
M client/galaxy/scripts/mvc/tool/tools-jobs.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/viz/trackster/tracks.js
M static/maps/mvc/annotation.js.map
M static/maps/mvc/app/app-analysis.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/tag.js.map
M static/maps/mvc/tool/tools-form-base.js.map
M static/maps/mvc/tool/tools-form-workflow.js.map
M static/maps/mvc/tool/tools-form.js.map
M static/maps/mvc/tool/tools-jobs.js.map
M static/maps/mvc/tool/tools-template.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/mvc/annotation.js
M static/scripts/mvc/app/app-analysis.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/tag.js
M static/scripts/mvc/tool/tools-form-base.js
M static/scripts/mvc/tool/tools-form-workflow.js
M static/scripts/mvc/tool/tools-form.js
M static/scripts/mvc/tool/tools-jobs.js
M static/scripts/mvc/tool/tools-template.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/viz/trackster/tracks.js
Log Message:
-----------
Webpack: normalize tags, annotations, and tools (change refs - 3 of 3)
Commit: 2956b12e9b292e42dfd2e2309b5c7d29b5b0d48b
https://github.com/galaxyproject/galaxy/commit/2956b12e9b292e42dfd2e2309b5c…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-13 (Fri, 13 Nov 2015)
Changed paths:
M client/galaxy/scripts/galaxy-app-base.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/citation/citation-model.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/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-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/job/job-model.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/tool/tools-form-workflow.js
M client/galaxy/scripts/mvc/tool/tools-jobs.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-select-ftp.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M static/maps/galaxy-app-base.js.map
M static/maps/galaxy.library.js.map
M static/maps/layout/masthead.js.map
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/citation/citation-model.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/history/history-content-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/job/job-model.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/library/library-model.js.map
M static/maps/mvc/tag.js.map
M static/maps/mvc/tool/tools-form-workflow.js.map
M static/maps/mvc/tool/tools-jobs.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-select-ftp.js.map
M static/maps/mvc/ui/ui-select-library.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/mvc/user/user-model.js.map
M static/maps/mvc/visualization/visualization-model.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-view-data.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/sweepster.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/visualization.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/galaxy-app-base.js
M static/scripts/galaxy.library.js
M static/scripts/layout/masthead.js
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/citation/citation-model.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/tag.js
M static/scripts/mvc/tool/tools-form-workflow.js
M static/scripts/mvc/tool/tools-jobs.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-select-ftp.js
M static/scripts/mvc/ui/ui-select-library.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/mvc/user/user-model.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-view-data.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/utils/utils.js
M static/scripts/viz/circster.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
M templates/user/logout.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Webpack: correct tool menu template loading in requirejs/galaxy.panels.mako by using require.config.map; normalize galaxy_config.root and Galaxy.options.root to Galaxy.root across the templates and js
Commit: b8870bfedc008d378481bd6740f31ff516271c16
https://github.com/galaxyproject/galaxy/commit/b8870bfedc008d378481bd6740f3…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-16 (Mon, 16 Nov 2015)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/trackster.less
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M static/maps/mvc/tool/tools.js.map
A static/maps/mvc/tools.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/mvc/tool/tools.js
A static/scripts/mvc/tools.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/trackster.css
M templates/admin/reload_tool.mako
M templates/show_params.mako
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/provision.yml
M test/docker/base/run_test_wrapper.sh
M test/docker/base/start_mysql.sh
M tools/data_source/upload.py
Log Message:
-----------
(merge dev)
Commit: bb089dfa424cefc64e65f1dd2aab5fe8fe1dad16
https://github.com/galaxyproject/galaxy/commit/bb089dfa424cefc64e65f1dd2aab…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-16 (Mon, 16 Nov 2015)
Changed paths:
M client/galaxy/scripts/galaxy-app-base.js
M static/maps/galaxy-app-base.js.map
M test/qunit/test-common.js
M test/qunit/tests/galaxy-app-base.js
Log Message:
-----------
Tests, qunit: fix import of underscore from libs, fix galaxy-app-base to not require config but have it passed in
Commit: 474a454958398bc3e70d16f7eaab5805aa89cf19
https://github.com/galaxyproject/galaxy/commit/474a454958398bc3e70d16f7eaab…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-16 (Mon, 16 Nov 2015)
Changed paths:
M client/galaxy/scripts/mvc/history/hda-model.js
M test/qunit/test-app.js
M test/qunit/test-common.js
M test/qunit/tests/workflow_editor_tests.js
Log Message:
-----------
Tests, qunit: galaxy_config.root->Galaxy.root, correct locations and shims of underscore and backbone in qunit tests
Commit: 7b93a53a4cbe671c40bb39849ae354938fffa284
https://github.com/galaxyproject/galaxy/commit/7b93a53a4cbe671c40bb39849ae3…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-17 (Tue, 17 Nov 2015)
Changed paths:
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/page.js
M client/galaxy/scripts/polyfills.js
M client/galaxy/scripts/utils/localization.js
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/layout/masthead.js.map
M static/maps/layout/page.js.map
M static/maps/polyfills.js.map
M static/maps/utils/localization.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/layout/masthead.js
M static/scripts/layout/page.js
M static/scripts/polyfills.js
M static/scripts/utils/localization.js
R static/style/blue/galaxy.frame.masthead.css
M templates/base/base_panels.mako
M templates/js-app.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M test/casperjs/api-history-permission-tests.js
Log Message:
-----------
Webpack: polyfill object.assign for phantomjs; remove galaxy.frame.masthead.css in favor of adding styles locally; change css load order to prevent 'ui-button' name collision between base and jquery-ui
Commit: d1d2f8388a4bc077275f535e41841158076a56de
https://github.com/galaxyproject/galaxy/commit/d1d2f8388a4bc077275f535e4184…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-18 (Wed, 18 Nov 2015)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/utils/query-string-parsing.js
M client/webpack.config.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/layout/masthead.js.map
M static/maps/layout/page.js.map
M static/maps/utils/query-string-parsing.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/layout/masthead.js
M static/scripts/layout/page.js
M static/scripts/utils/query-string-parsing.js
M templates/js-app.mako
Log Message:
-----------
Webpack: allow extending options from template call, add /login as app entry point for login app (still allowing user/login), add root/welcome and /login to allowed paths when require_login, fix None type error for redirect when visiting user/login directly, fix rendering of masthead, add query string to object util, correct job_id loading from index
Commit: 5eb9b206e798522fff1a9332e5d1a58c83528523
https://github.com/galaxyproject/galaxy/commit/5eb9b206e798522fff1a9332e5d1…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-18 (Wed, 18 Nov 2015)
Changed paths:
A client/galaxy/scripts/apps/login.js
A static/scripts/bundled/login.bundled.js
A static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Webpack: properly add login app to the repo
Commit: 17ec1b08fbc88c4960b94fbd19252c40e8a4e579
https://github.com/galaxyproject/galaxy/commit/17ec1b08fbc88c4960b94fbd1925…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-18 (Wed, 18 Nov 2015)
Changed paths:
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Webpack: add masthead div to galaxy.panels.mako as a target for replacement and becauseiamgoingcrazyfromtheeightdifferentwayswehavetorenderwebpages
Commit: 7cd5713dbb3acc82ee7c01f5110d37cb413392c8
https://github.com/galaxyproject/galaxy/commit/7cd5713dbb3acc82ee7c01f5110d…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-20 (Fri, 20 Nov 2015)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/webapps/galaxy/dataset/display.mako
M templates/webapps/galaxy/dataset/tabular_chunked.mako
M templates/webapps/galaxy/galaxy.panels.mako
M test/casperjs/spaceghost.js
Log Message:
-----------
Webpack: simplify query routes in analysis, remove duplicate js in display.mako and tabular_chunked.mako, change order of requirejs import; testing, casperjs: quiet requirejs scripterrors when navigating away from pages
Commit: 9c5d4cfc0e95966f8a41e8dedf83ea4b4793868e
https://github.com/galaxyproject/galaxy/commit/9c5d4cfc0e95966f8a41e8dedf83…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-20 (Fri, 20 Nov 2015)
Changed paths:
M client/galaxy/scripts/galaxy-app-base.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/app/app-login.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/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-view.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-view.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-listrow-view.js
M config/datatypes_conf.xml.sample
A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml
A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M config/plugins/interactive_environments/ipython/static/js/ipython.js
M config/plugins/interactive_environments/ipython/templates/ipython.mako
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M cron/build_chrom_db.py
M doc/source/admin/interactive_environments.rst
M doc/source/project/organization.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/test.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/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/remote_files.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/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.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/galaxy_install/tool_dependencies/recipe/tag_handler.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 run_tests.sh
M static/maps/galaxy-app-base.js.map
A static/maps/galaxy.menu.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/app/app-login.js.map
M static/maps/mvc/history/copy-dialog.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/galaxy.menu.js
M static/scripts/layout/menu.js
M static/scripts/mvc/app/app-login.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/copy-dialog.js
A static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/job/job-li.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/utils/utils.js
M test/api/helpers.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_workflow_extraction.py
M test/base/api.py
M test/base/interactor.py
M test/base/twilltestcase.py
A test/functional/tools/cheetah_problem_syntax_error.xml
A test/functional/tools/cheetah_problem_unbound_var.xml
A test/functional/tools/cheetah_problem_unbound_var_input.xml
A test/functional/tools/maxseconds.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/tools/test_tool_loader.py
Log Message:
-----------
(merge dev)
Commit: dba7e6640f816325c853fcc320e97c454a465bae
https://github.com/galaxyproject/galaxy/commit/dba7e6640f816325c853fcc320e9…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-20 (Fri, 20 Nov 2015)
Changed paths:
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/templates/compiled/panel_section.js
M client/galaxy/scripts/templates/compiled/tool_form.js
M client/galaxy/scripts/templates/compiled/tool_link.js
M client/galaxy/scripts/templates/compiled/tool_search.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/grunt-tasks/templates.js
M static/maps/layout/panel.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/templates/compiled/panel_section.js.map
M static/maps/templates/compiled/tool_form.js.map
M static/maps/templates/compiled/tool_link.js.map
M static/maps/templates/compiled/tool_search.js.map
M static/maps/viz/sweepster.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/layout/panel.js
M static/scripts/templates/compiled/panel_section.js
M static/scripts/templates/compiled/tool_form.js
M static/scripts/templates/compiled/tool_link.js
M static/scripts/templates/compiled/tool_search.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster/tracks.js
M templates/base/base_panels.mako
M templates/webapps/galaxy/visualization/sweepster.mako
Log Message:
-----------
Webpack: correct handlebars template generation to return an AMD function - this normalizes import of templates between webpack and require, fix sweepster tools import and templates
Commit: 51e098649070435570f9b68bf17ecc005da65bc2
https://github.com/galaxyproject/galaxy/commit/51e098649070435570f9b68bf17e…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-20 (Fri, 20 Nov 2015)
Changed paths:
A static/scripts/bundled/libs.bundled.js
A static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Webpack: add in the libs bundles, Carl. They're kinda important.
Commit: baeaae99059fc94ae2a0dc059cfd448d05bdcbbe
https://github.com/galaxyproject/galaxy/commit/baeaae99059fc94ae2a0dc059cfd…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-20 (Fri, 20 Nov 2015)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/galaxy.bundled.js
M static/scripts/bundled/galaxy.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:
-----------
Webpack: rebuild bundles using webpack 1.12.8 as defined in the package.json
Commit: f3f8fef28a55c7b4e6994b08e3125a0d66a36140
https://github.com/galaxyproject/galaxy/commit/f3f8fef28a55c7b4e6994b08e312…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-24 (Tue, 24 Nov 2015)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
R client/galaxy/scripts/apps/galaxy.js
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/apps/login.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/galaxy-app-base.js
M client/grunt-tasks/scripts.js
M client/webpack.config.js
M lib/galaxy/web/base/controller.py
M static/maps/galaxy-app-base.js.map
R static/maps/galaxy.menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
R static/scripts/bundled/galaxy.bundled.js
R static/scripts/bundled/galaxy.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/galaxy-app-base.js
R static/scripts/galaxy.menu.js
M templates/js-app.mako
Log Message:
-----------
Webpack: move Galaxy object creation from mako to app js, clean up and localize page, panels, and app
Commit: b15a4082939be8b533dddf9a6a63efec9be6b817
https://github.com/galaxyproject/galaxy/commit/b15a4082939be8b533dddf9a6a63…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-24 (Tue, 24 Nov 2015)
Changed paths:
R client/galaxy/scripts/tools/rgenetics/checkbox_and_radiobutton.js
R client/galaxy/scripts/tools/rgenetics/helper_functions.js
R client/galaxy/scripts/tools/rgenetics/timer.js
R static/maps/tools/rgenetics/checkbox_and_radiobutton.js.map
R static/maps/tools/rgenetics/helper_functions.js.map
R static/maps/tools/rgenetics/timer.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js
R static/scripts/tools/rgenetics/helper_functions.js
R static/scripts/tools/rgenetics/timer.js
Log Message:
-----------
Client: remove duplicate rgenetics directory tools/rgenetics
Commit: d921b4243101130d7de5517167eb38fa1aa6b1d3
https://github.com/galaxyproject/galaxy/commit/d921b4243101130d7de5517167eb…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-24 (Tue, 24 Nov 2015)
Changed paths:
R client/galaxy/scripts/mvc/app/app-analysis.js
R client/galaxy/scripts/mvc/app/app-login.js
R client/galaxy/scripts/mvc/app/app-view.js
R static/maps/mvc/app/app-analysis.js.map
R static/maps/mvc/app/app-login.js.map
R static/maps/mvc/app/app-view.js.map
R static/scripts/mvc/app/app-analysis.js
R static/scripts/mvc/app/app-login.js
R static/scripts/mvc/app/app-view.js
Log Message:
-----------
Webpack: remove mvc/app
Commit: 9f91b82245fc3ba467e8bef7b57bfc58ef02e9f0
https://github.com/galaxyproject/galaxy/commit/9f91b82245fc3ba467e8bef7b57b…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-24 (Tue, 24 Nov 2015)
Changed paths:
R client/galaxy/scripts/libs/IE/IE7.js
R client/galaxy/scripts/libs/IE/IE8.js
R client/galaxy/scripts/libs/IE/blank.gif
R client/galaxy/scripts/libs/IE/excanvas.js
R client/galaxy/scripts/libs/IE/ie7-recalc.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/mvc/workflow/workflow-connector.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/polyfills.js
M client/galaxy/scripts/viz/visualization.js
A static/incompatible-browser.html
R static/maps/libs/IE/IE7.js.map
R static/maps/libs/IE/IE8.js.map
R static/maps/libs/IE/excanvas.js.map
R static/maps/libs/IE/ie7-recalc.js.map
M static/maps/mvc/workflow/workflow-connector.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/polyfills.js.map
M static/maps/viz/visualization.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
R static/scripts/libs/IE/IE7.js
R static/scripts/libs/IE/IE8.js
R static/scripts/libs/IE/blank.gif
R static/scripts/libs/IE/excanvas.js
R static/scripts/libs/IE/ie7-recalc.js
M static/scripts/mvc/workflow/workflow-connector.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/polyfills.js
M static/scripts/viz/visualization.js
M templates/webapps/galaxy/visualization/display.mako
M templates/webapps/galaxy/visualization/display_in_frame.mako
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Client: remove IE7/8 and excanvas polyfills
Commit: e3e9579a812c468fba3f8a64fae7c7455e4b5a9e
https://github.com/galaxyproject/galaxy/commit/e3e9579a812c468fba3f8a64fae7…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-24 (Tue, 24 Nov 2015)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/login.js
R client/galaxy/scripts/galaxy-app-base.js
A client/galaxy/scripts/galaxy.js
R static/maps/galaxy-app-base.js.map
A static/maps/galaxy.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
R static/scripts/galaxy-app-base.js
A static/scripts/galaxy.js
M templates/galaxy_client_app.mako
Log Message:
-----------
Webpack: pack scripts, move galaxy-app-base.js to galaxy.js
Commit: 68da0004709e88ed8a856d39e9fa4e64aa3bc653
https://github.com/galaxyproject/galaxy/commit/68da0004709e88ed8a856d39e9fa…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-25 (Wed, 25 Nov 2015)
Changed paths:
R client/galaxy/scripts/rgenetics/checkbox_and_radiobutton.js
R client/galaxy/scripts/rgenetics/helper_functions.js
R client/galaxy/scripts/rgenetics/timer.js
R static/maps/rgenetics/checkbox_and_radiobutton.js.map
R static/maps/rgenetics/helper_functions.js.map
R static/maps/rgenetics/timer.js.map
R static/scripts/rgenetics/checkbox_and_radiobutton.js
R static/scripts/rgenetics/helper_functions.js
R static/scripts/rgenetics/timer.js
Log Message:
-----------
Client, rgenetics: 'Nuke 'em all' - R.Lazarus
Commit: f397584538f59d03d9c37d3f9366b455022e97b2
https://github.com/galaxyproject/galaxy/commit/f397584538f59d03d9c37d3f9366…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-11-25 (Wed, 25 Nov 2015)
Changed paths:
M client/galaxy/scripts/polyfills.js
M static/maps/polyfills.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/polyfills.js
M templates/base.mako
M templates/base/base_panels.mako
M templates/js-app.mako
Log Message:
-----------
Webpack: add link rel='index' with href to Galaxy.root, rework browser testing to use the same when redirecting to error pages
Commit: 002bc6b40a4314fc5f35f6156a73cad91532484d
https://github.com/galaxyproject/galaxy/commit/002bc6b40a4314fc5f35f6156a73…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-12-02 (Wed, 02 Dec 2015)
Changed paths:
M .gitignore
M client/GruntFile.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/dataset/dataset-li.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-view.js
M client/galaxy/scripts/mvc/tool/tools-form-base.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/grunt-tasks/style.js
M client/package.json
M config/datatypes_conf.xml.sample
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/visualizations/charts/templates/charts.mako
A config/reports.ini.sample
R config/reports_wsgi.ini.sample
M config/tool_shed.ini.sample
A doc/source/releases/15.10.rst
M doc/source/releases/15.10_announce.rst
A doc/source/releases/16.01_announce.rst
M lib/galaxy/datatypes/interval.py
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/shed_util_common.py
M run_reports.sh
M scripts/bootstrap_history.py
M scripts/functional_tests.py
M scripts/sync_reports_config.py
M static/maps/layout/masthead.js.map
M static/maps/layout/panel.js.map
M static/maps/layout/scratchbook.js.map
M static/maps/mvc/base-mvc.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
A static/maps/mvc/list/list-panel.js.map
M static/maps/mvc/list/list-view.js.map
M static/maps/mvc/tool/tools-form-base.js.map
A static/maps/mvc/tools/tools-form-base.js.map
M static/maps/mvc/ui/ui-buttons.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/panel.js
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/base-mvc.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tool/tools-form-base.js
A static/scripts/mvc/tools/tools-form-base.js
M static/scripts/mvc/ui/ui-buttons.js
M static/style/blue/autocomplete_tagging.css
M static/style/blue/base.css
M static/style/blue/embed_item.css
M static/style/blue/iphone.css
M static/style/blue/library.css
M static/style/blue/trackster.css
M templates/webapps/galaxy/root/index.mako
M templates/webapps/galaxy/workflow/run.mako
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
A test/api/workflows_format_2/README.txt
A test/api/workflows_format_2/__init__.py
A test/api/workflows_format_2/converter.py
A test/api/workflows_format_2/interface.py
A test/api/workflows_format_2/main.py
R test/api/yaml_to_workflow.py
A test/functional/tools/collection_type_source.xml
A test/functional/tools/output_format_collection.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/simple_constructs.yml
M test/qunit/package.json
M test/unit/tools/test_actions.py
M test/unit/tools/test_parsing.py
Log Message:
-----------
(merge dev)
Commit: cfdbf8c0e71c5cdfa0ae47f6da7cc4553efd8429
https://github.com/galaxyproject/galaxy/commit/cfdbf8c0e71c5cdfa0ae47f6da7c…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-12-02 (Wed, 02 Dec 2015)
Changed paths:
M test/qunit/test-app.js
M test/qunit/test-data/bootstrapped.js
M test/qunit/tests/galaxy-app-base.js
Log Message:
-----------
Testing, webpack: correct name of Galaxy module in qunit, properly call require, pass GalaxyApp data
Commit: 963d8637e869a214ee0e2c352a8184feb980a40e
https://github.com/galaxyproject/galaxy/commit/963d8637e869a214ee0e2c352a81…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-12-02 (Wed, 02 Dec 2015)
Changed paths:
R client/galaxy/scripts/galaxy.tools.js
R static/maps/galaxy.tools.js.map
R static/maps/galaxy.workflows.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
R static/scripts/galaxy.tools.js
R static/scripts/galaxy.workflows.js
Log Message:
-----------
Webpack: remove cruft galaxy.tools.js and (remnants of) galaxy.workflows.js
Commit: a3e3bde6a2b5c2fc9433336526ec32badfc8ce9d
https://github.com/galaxyproject/galaxy/commit/a3e3bde6a2b5c2fc9433336526ec…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M client/galaxy/scripts/apps/login.js
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M static/scripts/bundled/analysis.bundled.js.map
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:
-----------
Webpack: restore redirect for after login when require_login; remove allowed_paths for require_login: /index, /tool_menu, /masthead, library/browse, history/list, dataset/list
Commit: b72035c9fc4136af5f3db464fd5b2a9c5e330cca
https://github.com/galaxyproject/galaxy/commit/b72035c9fc4136af5f3db464fd5b…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M static/maps/layout/masthead.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view-edit-current.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/mvc/history/history-model.js
M static/scripts/mvc/history/history-view-edit-current.js
Log Message:
-----------
Webpack: fix/re-work the pub-sub connection between the quotameter and the history panel so that the meter updates properly when a new dataset is added
Commit: f40d4fc178cbf3a3266a56ce0108b87e21bd5be0
https://github.com/galaxyproject/galaxy/commit/f40d4fc178cbf3a3266a56ce0108…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M config/galaxy.ini.sample
R templates/webapps/galaxy/root/index.mako
Log Message:
-----------
Webpack: re-add show_welcome_with_login config option (lost due to merge/gitignore?); remove root/index.mako
Commit: 9e8068f3671cdef499ed51aca3869f91e2e5b69d
https://github.com/galaxyproject/galaxy/commit/9e8068f3671cdef499ed51aca386…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M README.rst
M client/galaxy/scripts/mvc/history/options-menu.js
M config/datatypes_conf.xml.sample
A config/dependency_resolvers_conf.xml.sample
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/test.idpDB
A lib/galaxy/datatypes/test/test.mz5
A lib/galaxy/datatypes/triples.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/execute.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/api/repositories.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/migrate/check.py
M run_tests.sh
M static/maps/mvc/history/options-menu.js.map
M static/scripts/mvc/history/options-menu.js
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
M test/api/helpers.py
M test/api/test_jobs.py
M test/api/test_workflows.py
A test/functional/tools/create_10.xml
M test/functional/tools/samples_tool_conf.xml
M test/qunit/test-common.js
M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml
M test/unit/test_galaxy_mapping.py
M test/unit/workflows/test_render.py
A test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
Log Message:
-----------
(merge dev)
Commit: 9f8eb465e718d4b643120e8554d119702c264135
https://github.com/galaxyproject/galaxy/commit/9f8eb465e718d4b643120e8554d1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M .gitignore
A client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/apps/history-panel.js
A client/galaxy/scripts/apps/login.js
A client/galaxy/scripts/apps/tool-panel.js
R client/galaxy/scripts/base.js
R client/galaxy/scripts/galaxy-app-base.js
R client/galaxy/scripts/galaxy.autocom_tagging.js
R client/galaxy/scripts/galaxy.base.js
R client/galaxy/scripts/galaxy.frame.js
A client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
R client/galaxy/scripts/galaxy.masthead.js
R client/galaxy/scripts/galaxy.menu.js
M client/galaxy/scripts/galaxy.pages.js
R client/galaxy/scripts/galaxy.panels.js
R client/galaxy/scripts/galaxy.tools.js
R client/galaxy/scripts/galaxy.ui.scrollPanel.js
A client/galaxy/scripts/layout/masthead.js
A client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/layout/modal.js
A client/galaxy/scripts/layout/page.js
A client/galaxy/scripts/layout/panel.js
A client/galaxy/scripts/layout/scratchbook.js
R client/galaxy/scripts/libs/IE/IE7.js
R client/galaxy/scripts/libs/IE/IE8.js
R client/galaxy/scripts/libs/IE/blank.gif
R client/galaxy/scripts/libs/IE/excanvas.js
R client/galaxy/scripts/libs/IE/ie7-recalc.js
A client/galaxy/scripts/libs/backbone.js
R client/galaxy/scripts/libs/backbone/backbone.js
M client/galaxy/scripts/libs/d3.js
A client/galaxy/scripts/mvc/annotation.js
R client/galaxy/scripts/mvc/annotations.js
R client/galaxy/scripts/mvc/app/app-analysis.js
R client/galaxy/scripts/mvc/app/app-login.js
R client/galaxy/scripts/mvc/app/app-view.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/collection/collection-model.js
R client/galaxy/scripts/mvc/collection/collection-panel-edit.js
R client/galaxy/scripts/mvc/collection/collection-panel.js
A client/galaxy/scripts/mvc/collection/collection-view-edit.js
A client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
R client/galaxy/scripts/mvc/data.js
A client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-list.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/grid/grid-view.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/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
R client/galaxy/scripts/mvc/history/history-panel-annotated.js
R client/galaxy/scripts/mvc/history/history-panel-edit-current.js
R client/galaxy/scripts/mvc/history/history-panel-edit.js
R client/galaxy/scripts/mvc/history/history-panel.js
A client/galaxy/scripts/mvc/history/history-view-annotated.js
A client/galaxy/scripts/mvc/history/history-view-edit-current.js
A client/galaxy/scripts/mvc/history/history-view-edit.js
A 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/job/job-model.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-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/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
R client/galaxy/scripts/mvc/list/list-panel.js
A client/galaxy/scripts/mvc/list/list-view.js
A client/galaxy/scripts/mvc/tag.js
R client/galaxy/scripts/mvc/tags.js
A client/galaxy/scripts/mvc/tool/tools-form-base.js
A client/galaxy/scripts/mvc/tool/tools-form-workflow.js
A client/galaxy/scripts/mvc/tool/tools-form.js
A client/galaxy/scripts/mvc/tool/tools-jobs.js
A client/galaxy/scripts/mvc/tool/tools-template.js
A client/galaxy/scripts/mvc/tool/tools.js
R client/galaxy/scripts/mvc/tools.js
R client/galaxy/scripts/mvc/tools/tools-form-base.js
R client/galaxy/scripts/mvc/tools/tools-form-workflow.js
R client/galaxy/scripts/mvc/tools/tools-form.js
R client/galaxy/scripts/mvc/tools/tools-jobs.js
R client/galaxy/scripts/mvc/tools/tools-template.js
M client/galaxy/scripts/mvc/ui/ui-select-ftp.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/workflow/workflow-connector.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
A client/galaxy/scripts/onload.js
A client/galaxy/scripts/polyfills.js
R client/galaxy/scripts/rgenetics/checkbox_and_radiobutton.js
R client/galaxy/scripts/rgenetics/helper_functions.js
R client/galaxy/scripts/rgenetics/timer.js
M client/galaxy/scripts/templates/compiled/panel_section.js
M client/galaxy/scripts/templates/compiled/tool_form.js
M client/galaxy/scripts/templates/compiled/tool_link.js
M client/galaxy/scripts/templates/compiled/tool_search.js
R client/galaxy/scripts/tools/rgenetics/checkbox_and_radiobutton.js
R client/galaxy/scripts/tools/rgenetics/helper_functions.js
R client/galaxy/scripts/tools/rgenetics/timer.js
A client/galaxy/scripts/ui/autocom_tagging.js
A client/galaxy/scripts/ui/editable-text.js
A client/galaxy/scripts/ui/popupmenu.js
A client/galaxy/scripts/ui/scroll-panel.js
A client/galaxy/scripts/utils/async-save-text.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/trackster/util.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/style/less/base.less
M client/grunt-tasks/install-libs.js
M client/grunt-tasks/scripts.js
M client/grunt-tasks/templates.js
M client/package.json
A client/webpack.config.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/users.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/root.py
A static/incompatible-browser.html
R static/maps/base.js.map
R static/maps/galaxy-app-base.js.map
R static/maps/galaxy.autocom_tagging.js.map
R static/maps/galaxy.base.js.map
R static/maps/galaxy.frame.js.map
A static/maps/galaxy.js.map
M static/maps/galaxy.library.js.map
R static/maps/galaxy.masthead.js.map
R static/maps/galaxy.menu.js.map
M static/maps/galaxy.pages.js.map
R static/maps/galaxy.panels.js.map
R static/maps/galaxy.tools.js.map
R static/maps/galaxy.ui.scrollPanel.js.map
R static/maps/galaxy.workflows.js.map
A static/maps/layout/masthead.js.map
A static/maps/layout/menu.js.map
A static/maps/layout/modal.js.map
A static/maps/layout/page.js.map
A static/maps/layout/panel.js.map
A static/maps/layout/scratchbook.js.map
R static/maps/libs/IE/IE7.js.map
R static/maps/libs/IE/IE8.js.map
R static/maps/libs/IE/excanvas.js.map
R static/maps/libs/IE/ie7-recalc.js.map
A static/maps/libs/backbone.js.map
A static/maps/libs/common-libs.js.map
A static/maps/mvc/annotation.js.map
R static/maps/mvc/annotations.js.map
R static/maps/mvc/app/app-analysis.js.map
R static/maps/mvc/app/app-login.js.map
R static/maps/mvc/app/app-view.js.map
M static/maps/mvc/base-mvc.js.map
M static/maps/mvc/citation/citation-model.js.map
M static/maps/mvc/collection/collection-model.js.map
R static/maps/mvc/collection/collection-panel-edit.js.map
R static/maps/mvc/collection/collection-panel.js.map
A static/maps/mvc/collection/collection-view-edit.js.map
A static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
R static/maps/mvc/data.js.map
A static/maps/mvc/dataset/data.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-list.js.map
M static/maps/mvc/dataset/dataset-model.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/history-content-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
R static/maps/mvc/history/history-panel-annotated.js.map
R static/maps/mvc/history/history-panel-edit-current.js.map
R static/maps/mvc/history/history-panel-edit.js.map
R static/maps/mvc/history/history-panel.js.map
A static/maps/mvc/history/history-view-annotated.js.map
A static/maps/mvc/history/history-view-edit-current.js.map
A static/maps/mvc/history/history-view-edit.js.map
A static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/job/job-model.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/library/library-model.js.map
A static/maps/mvc/list/list-view.js.map
A static/maps/mvc/tag.js.map
R static/maps/mvc/tags.js.map
A static/maps/mvc/tool/tools-form-base.js.map
A static/maps/mvc/tool/tools-form-workflow.js.map
A static/maps/mvc/tool/tools-form.js.map
A static/maps/mvc/tool/tools-jobs.js.map
A static/maps/mvc/tool/tools-template.js.map
A static/maps/mvc/tool/tools.js.map
R static/maps/mvc/tools/tools-form-workflow.js.map
R static/maps/mvc/tools/tools-form.js.map
R static/maps/mvc/tools/tools-jobs.js.map
R static/maps/mvc/tools/tools-template.js.map
M static/maps/mvc/ui/ui-select-ftp.js.map
M static/maps/mvc/ui/ui-select-library.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/mvc/user/user-model.js.map
M static/maps/mvc/visualization/visualization-model.js.map
M static/maps/mvc/workflow/workflow-connector.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-view-data.js.map
M static/maps/mvc/workflow/workflow-view.js.map
A static/maps/onload.js.map
A static/maps/polyfills.js.map
R static/maps/rgenetics/checkbox_and_radiobutton.js.map
R static/maps/rgenetics/helper_functions.js.map
R static/maps/rgenetics/timer.js.map
M static/maps/templates/compiled/panel_section.js.map
M static/maps/templates/compiled/tool_form.js.map
M static/maps/templates/compiled/tool_link.js.map
M static/maps/templates/compiled/tool_search.js.map
R static/maps/tools/rgenetics/checkbox_and_radiobutton.js.map
R static/maps/tools/rgenetics/helper_functions.js.map
R static/maps/tools/rgenetics/timer.js.map
A static/maps/ui/autocom_tagging.js.map
A static/maps/ui/editable-text.js.map
A static/maps/ui/popupmenu.js.map
A static/maps/ui/scroll-panel.js.map
A static/maps/utils/async-save-text.js.map
M static/maps/utils/localization.js.map
M static/maps/utils/query-string-parsing.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/sweepster.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/trackster/util.js.map
M static/maps/viz/visualization.js.map
R static/scripts/base.js
A static/scripts/bundled/analysis.bundled.js
A static/scripts/bundled/analysis.bundled.js.map
A static/scripts/bundled/libs.bundled.js
A static/scripts/bundled/libs.bundled.js.map
A static/scripts/bundled/login.bundled.js
A static/scripts/bundled/login.bundled.js.map
R static/scripts/galaxy-app-base.js
R static/scripts/galaxy.autocom_tagging.js
R static/scripts/galaxy.base.js
R static/scripts/galaxy.frame.js
A static/scripts/galaxy.js
M static/scripts/galaxy.library.js
R static/scripts/galaxy.masthead.js
R static/scripts/galaxy.menu.js
M static/scripts/galaxy.pages.js
R static/scripts/galaxy.panels.js
R static/scripts/galaxy.tools.js
R static/scripts/galaxy.ui.scrollPanel.js
R static/scripts/galaxy.workflows.js
A static/scripts/layout/masthead.js
A static/scripts/layout/menu.js
A static/scripts/layout/modal.js
A static/scripts/layout/page.js
A static/scripts/layout/panel.js
A static/scripts/layout/scratchbook.js
R static/scripts/libs/IE/IE7.js
R static/scripts/libs/IE/IE8.js
R static/scripts/libs/IE/blank.gif
R static/scripts/libs/IE/excanvas.js
R static/scripts/libs/IE/ie7-recalc.js
A static/scripts/libs/backbone.js
A static/scripts/libs/common-libs.js
A static/scripts/mvc/annotation.js
R static/scripts/mvc/annotations.js
R static/scripts/mvc/app/app-analysis.js
R static/scripts/mvc/app/app-login.js
R static/scripts/mvc/app/app-view.js
M static/scripts/mvc/base-mvc.js
M static/scripts/mvc/citation/citation-model.js
M static/scripts/mvc/collection/collection-model.js
R static/scripts/mvc/collection/collection-panel-edit.js
R static/scripts/mvc/collection/collection-panel.js
A static/scripts/mvc/collection/collection-view-edit.js
A static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
R static/scripts/mvc/data.js
A static/scripts/mvc/dataset/data.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-list.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
R static/scripts/mvc/history/history-panel-annotated.js
R static/scripts/mvc/history/history-panel-edit-current.js
R static/scripts/mvc/history/history-panel-edit.js
A static/scripts/mvc/history/history-view-annotated.js
A static/scripts/mvc/history/history-view-edit-current.js
A static/scripts/mvc/history/history-view-edit.js
A static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
R static/scripts/mvc/list/list-panel.js
A static/scripts/mvc/list/list-view.js
A static/scripts/mvc/tag.js
R static/scripts/mvc/tags.js
A static/scripts/mvc/tool/tools-form-base.js
A static/scripts/mvc/tool/tools-form-workflow.js
A static/scripts/mvc/tool/tools-form.js
A static/scripts/mvc/tool/tools-jobs.js
A static/scripts/mvc/tool/tools-template.js
A static/scripts/mvc/tool/tools.js
R static/scripts/mvc/tools/tools-form-workflow.js
R static/scripts/mvc/tools/tools-form.js
R static/scripts/mvc/tools/tools-jobs.js
R static/scripts/mvc/tools/tools-template.js
M static/scripts/mvc/ui/ui-select-ftp.js
M static/scripts/mvc/ui/ui-select-library.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/mvc/user/user-model.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/workflow/workflow-connector.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-view-data.js
M static/scripts/mvc/workflow/workflow-view.js
A static/scripts/onload.js
A static/scripts/polyfills.js
R static/scripts/rgenetics/checkbox_and_radiobutton.js
R static/scripts/rgenetics/helper_functions.js
R static/scripts/rgenetics/timer.js
M static/scripts/templates/compiled/panel_section.js
M static/scripts/templates/compiled/tool_form.js
M static/scripts/templates/compiled/tool_link.js
M static/scripts/templates/compiled/tool_search.js
R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js
R static/scripts/tools/rgenetics/helper_functions.js
R static/scripts/tools/rgenetics/timer.js
A static/scripts/ui/autocom_tagging.js
A static/scripts/ui/editable-text.js
A static/scripts/ui/popupmenu.js
A static/scripts/ui/scroll-panel.js
A static/scripts/utils/async-save-text.js
M static/scripts/utils/localization.js
M static/scripts/utils/query-string-parsing.js
M static/scripts/utils/utils.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/trackster/util.js
M static/scripts/viz/visualization.js
M static/style/blue/base.css
R static/style/blue/galaxy.frame.masthead.css
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/galaxy_client_app.mako
M templates/grid_base.mako
A templates/js-app.mako
M templates/refresh_frames.mako
M templates/tagging_common.mako
M templates/user/logout.mako
M templates/webapps/galaxy/dataset/display.mako
M templates/webapps/galaxy/dataset/edit_attributes.mako
M templates/webapps/galaxy/dataset/tabular_chunked.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/history/view_multiple.mako
M templates/webapps/galaxy/library/common/ldda_edit_info.mako
M templates/webapps/galaxy/library/common/move_library_item.mako
M templates/webapps/galaxy/library/common/upload.mako
M templates/webapps/galaxy/page/editor.mako
M templates/webapps/galaxy/requests/common/create_request.mako
M templates/webapps/galaxy/requests/common/find_samples.mako
R templates/webapps/galaxy/root/index.mako
M templates/webapps/galaxy/visualization/display.mako
M templates/webapps/galaxy/visualization/display_in_frame.mako
M templates/webapps/galaxy/visualization/sweepster.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/galaxy/workflow/run.mako
M test/casperjs/api-history-permission-tests.js
M test/casperjs/spaceghost.js
M test/qunit/test-app.js
M test/qunit/test-common.js
M test/qunit/test-data/bootstrapped.js
M test/qunit/tests/galaxy-app-base.js
M test/qunit/tests/workflow_editor_tests.js
Log Message:
-----------
Merge pull request #1144 from carlfeberhard/webpack
Webpack
Compare: https://github.com/galaxyproject/galaxy/compare/3e8b58c5aa66...9f8eb465e718
1
0
Branch: refs/heads/release_15.10
Home: https://github.com/galaxyproject/galaxy
Commit: f08d518aa0bfee1ba3d3da1cca410eee77446534
https://github.com/galaxyproject/galaxy/commit/f08d518aa0bfee1ba3d3da1cca41…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Use fixed path to sync like in dev.
It keeps picking up something else on my PATH and breaking my tests when I switch to release_15.10.
Commit: f34d70101910dcdd6d699dc1f8688f69ea6d97cf
https://github.com/galaxyproject/galaxy/commit/f34d70101910dcdd6d699dc1f868…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Merge pull request #1242 from jmchilton/sync_path
[15.10] Use fixed path to sync like in dev.
Compare: https://github.com/galaxyproject/galaxy/compare/736bf3ce843d...f34d70101910
1
0
[galaxyproject/galaxy] 107de0: Add the missing "amqp_ack_republish_time" param fo...
by GitHub 04 Dec '15
by GitHub 04 Dec '15
04 Dec '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 107de0e1d77200dbd8ac6bc94359f424a25ebca8
https://github.com/galaxyproject/galaxy/commit/107de0e1d77200dbd8ac6bc94359…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M lib/galaxy/jobs/runners/pulsar.py
Log Message:
-----------
Add the missing "amqp_ack_republish_time" param for the Pulsar runner
(it's available in the Pulsar client lib).
Commit: 736bf3ce843daef3af1fef10ed8441c5ebe65603
https://github.com/galaxyproject/galaxy/commit/736bf3ce843daef3af1fef10ed84…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M lib/galaxy/jobs/runners/pulsar.py
Log Message:
-----------
Merge pull request #1234 from natefoo/pulsar-missing-param
[15.10] Add the missing "amqp_ack_republish_time" param for the Pulsar runner
Commit: 3e8b58c5aa66da83206230d27aacba1eaa7faa00
https://github.com/galaxyproject/galaxy/commit/3e8b58c5aa66da83206230d27aac…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M lib/galaxy/jobs/runners/pulsar.py
Log Message:
-----------
Merge branch 'release_15.10' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/5675617178b6...3e8b58c5aa66
1
0
[galaxyproject/galaxy] 107de0: Add the missing "amqp_ack_republish_time" param fo...
by GitHub 04 Dec '15
by GitHub 04 Dec '15
04 Dec '15
Branch: refs/heads/release_15.10
Home: https://github.com/galaxyproject/galaxy
Commit: 107de0e1d77200dbd8ac6bc94359f424a25ebca8
https://github.com/galaxyproject/galaxy/commit/107de0e1d77200dbd8ac6bc94359…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M lib/galaxy/jobs/runners/pulsar.py
Log Message:
-----------
Add the missing "amqp_ack_republish_time" param for the Pulsar runner
(it's available in the Pulsar client lib).
Commit: 736bf3ce843daef3af1fef10ed8441c5ebe65603
https://github.com/galaxyproject/galaxy/commit/736bf3ce843daef3af1fef10ed84…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M lib/galaxy/jobs/runners/pulsar.py
Log Message:
-----------
Merge pull request #1234 from natefoo/pulsar-missing-param
[15.10] Add the missing "amqp_ack_republish_time" param for the Pulsar runner
Compare: https://github.com/galaxyproject/galaxy/compare/516b079ab97d...736bf3ce843d
1
0
04 Dec '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1cc57b1eb2c295dbd68837c864740b6ff079b83d
https://github.com/galaxyproject/galaxy/commit/1cc57b1eb2c295dbd68837c86474…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Add icons and reorganise history menu
Commit: 564f12c50ffaed386f57e1fd2d4048840e5f8288
https://github.com/galaxyproject/galaxy/commit/564f12c50ffaed386f57e1fd2d40…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Remove icons
Commit: 42b6da87554b78fddd5b592a82d46deb83cada15
https://github.com/galaxyproject/galaxy/commit/42b6da87554b78fddd5b592a82d4…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
Log Message:
-----------
Comment out debugging
Commit: 9bd2712c5d9aa260012ffdad267434758bf086c0
https://github.com/galaxyproject/galaxy/commit/9bd2712c5d9aa260012ffdad2674…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M static/maps/mvc/history/options-menu.js.map
M static/scripts/libs/jquery/jquery.dynatree.js
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Just going to clobber everything
Commit: 198cb7c9a1534e7914ca76c4648fd750234ddb9f
https://github.com/galaxyproject/galaxy/commit/198cb7c9a1534e7914ca76c4648f…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M static/scripts/libs/jquery/jquery.dynatree.js
Log Message:
-----------
Fix rebase issue
Commit: 5675617178b6d103de88ff907d137974b908761e
https://github.com/galaxyproject/galaxy/commit/5675617178b6d103de88ff907d13…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Merge pull request #985 from erasche/nicer-history-menu
Add icons and reorganise history menu
Compare: https://github.com/galaxyproject/galaxy/compare/4d396a6945b3...5675617178b6
1
0
04 Dec '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 69b8d83ba2b829621183361694f341bda66a77fe
https://github.com/galaxyproject/galaxy/commit/69b8d83ba2b829621183361694f3…
Author: Peter van Heusden <pvh(a)sanbi.ac.za>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/tools/deps/resolvers/modules.py
Log Message:
-----------
* Make default_indicator configurable
* Document classes
Commit: b87c22c73b9a3f6d31507d268e945a6ae8deef60
https://github.com/galaxyproject/galaxy/commit/b87c22c73b9a3f6d31507d268e94…
Author: Peter van Heusden <pvh(a)sanbi.ac.za>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
A config/dependency_resolvers_conf.xml.sample
Log Message:
-----------
* Add sample dependency_resolvers_conf.xml that matches actual default
Commit: 56054c6d98519541b896a5145998b02688750bb6
https://github.com/galaxyproject/galaxy/commit/56054c6d98519541b896a5145998…
Author: Peter van Heusden <pvh(a)sanbi.ac.za>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/tools/deps/resolvers/modules.py
Log Message:
-----------
* Fix AvailModuleChecker() invocation and propogate default default_indicator
Commit: bd0663f65062d60de810478566604b3ee33b109d
https://github.com/galaxyproject/galaxy/commit/bd0663f65062d60de81047856660…
Author: Peter van Heusden <pvh(a)sanbi.ac.za>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/tools/deps/resolvers/modules.py
Log Message:
-----------
* Initialise default_indicator before using __modules
Commit: ba3e3da946b699a03ef9cab9095ea294d6df3b69
https://github.com/galaxyproject/galaxy/commit/ba3e3da946b699a03ef9cab9095e…
Author: Peter van Heusden <pvh(a)sanbi.ac.za>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
Log Message:
-----------
* Add sample config for modules resolver
Commit: 6f727962945481b75dd675e70eed78e8b785cb0a
https://github.com/galaxyproject/galaxy/commit/6f727962945481b75dd675e70eed…
Author: Peter van Heusden <pvh(a)sanbi.ac.za>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
Log Message:
-----------
* Update sample config for modules resolver
Commit: 4d396a6945b3394cd529849076b1f6c9892962c5
https://github.com/galaxyproject/galaxy/commit/4d396a6945b3394cd529849076b1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
A config/dependency_resolvers_conf.xml.sample
M lib/galaxy/tools/deps/resolvers/modules.py
Log Message:
-----------
Merge pull request #1221 from pvanheus/env-modules-resolve
Add documentation and extra options to Environment Modules resolver
Compare: https://github.com/galaxyproject/galaxy/compare/4289cf3ab2f9...4d396a6945b3
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0eb87f911c4523ecb268b26ad8c74a0252ce8453
https://github.com/galaxyproject/galaxy/commit/0eb87f911c4523ecb268b26ad8c7…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Minor docstring typo
Commit: 4289cf3ab2f92375e6e4d9751064325b55cceaae
https://github.com/galaxyproject/galaxy/commit/4289cf3ab2f92375e6e4d9751064…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Merge pull request #1235 from blankenberg/typo_dev
Minor docstring typo
Compare: https://github.com/galaxyproject/galaxy/compare/905471e32fef...4289cf3ab2f9
1
0
[galaxyproject/galaxy] 1adff9: Wait on jobs and history in certain API test cases...
by GitHub 04 Dec '15
by GitHub 04 Dec '15
04 Dec '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1adff983f2509e6551f9000008d614a61d9b12a6
https://github.com/galaxyproject/galaxy/commit/1adff983f2509e6551f9000008d6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M test/api/helpers.py
M test/api/test_jobs.py
Log Message:
-----------
Wait on jobs and history in certain API test cases.
This strategy proved to work around certain race conditions in tool testing so hopefully it will solve the transiently failing job searching and filtering test cases.
Commit: 905471e32fef02b9da38d2efe0cc463cd258cbff
https://github.com/galaxyproject/galaxy/commit/905471e32fef02b9da38d2efe0cc…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-04 (Fri, 04 Dec 2015)
Changed paths:
M test/api/helpers.py
M test/api/test_jobs.py
Log Message:
-----------
Merge pull request #1226 from jmchilton/jobs_api_test_fix
Wait on jobs and history in certain API test cases.
Compare: https://github.com/galaxyproject/galaxy/compare/5c87d07e0f53...905471e32fef
1
0