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November 2015
- 2 participants
- 160 discussions
[galaxyproject/galaxy] d20677: Fix Remote User failures due to apache null header...
by GitHub 03 Nov '15
by GitHub 03 Nov '15
03 Nov '15
Branch: refs/heads/release_15.10
Home: https://github.com/galaxyproject/galaxy
Commit: d20677bb640de726574ae7f3e8d86739a8702cb5
https://github.com/galaxyproject/galaxy/commit/d20677bb640de726574ae7f3e8d8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Fix Remote User failures due to apache null headers.
Commit: 3b8edf6aebfb10d1b52b57701eb4cb07558e9c9e
https://github.com/galaxyproject/galaxy/commit/3b8edf6aebfb10d1b52b57701eb4…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-11-03 (Tue, 03 Nov 2015)
Changed paths:
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Merge pull request #1003 from dannon/remote_user_apache_fix
[15.10] Fix Remote User failures due to apache null headers.
Compare: https://github.com/galaxyproject/galaxy/compare/3b133d0d9206...3b8edf6aebfb
1
0
03 Nov '15
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 58fab7545f5b61a23f61dbd0788379f04ba9bbf3
https://github.com/galaxyproject/usegalaxy-playbook/commit/58fab7545f5b61a2…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-11-03 (Tue, 03 Nov 2015)
Changed paths:
M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py
M files/galaxy/common/dynamic_rules/reserved.py
Log Message:
-----------
Add Dan to reserved node users
1
0
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: f2cff9c9f1700c23e2280bde7b1b0578386df261
https://github.com/galaxyproject/usegalaxy-playbook/commit/f2cff9c9f1700c23…
Author: tnabtaf <clements(a)galaxyproject.org>
Date: 2015-11-02 (Mon, 02 Nov 2015)
Changed paths:
A files/galaxy/common/static/welcome_img/GCC2016TrVote.png
A files/galaxy/common/static/welcome_img/MississippiGalaxy.png
M templates/galaxy/common/static/welcome.html.j2
Log Message:
-----------
Updated slide rotation.
1
0
02 Nov '15
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 01cd5c650d6be4c6f75934de976e157826d74279
https://github.com/galaxyproject/infrastructure-playbook/commit/01cd5c650d6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-20 (Tue, 20 Oct 2015)
Changed paths:
M common_roles
Log Message:
-----------
Update common roles.
Commit: cf8a746f22e3596590a675729df9575f541cf504
https://github.com/galaxyproject/infrastructure-playbook/commit/cf8a746f22e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-11-02 (Mon, 02 Nov 2015)
Changed paths:
M common_roles
A galaxyenv/group_vars/baseenv.yml
M galaxyenv/host_vars/orval.galaxyproject.org.yml
M galaxyenv/secret_group_vars/all.yml
M galaxyenv/secret_host_vars/n2.galaxyproject.org.yml
M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml
Log Message:
-----------
depot stuff I forgot to commit + add Dannon to sites@orval
Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/577c599fa6…
1
0
[galaxyproject/galaxy] 8b630d: Update galaxy.jobs.runners.util from pulsar.manage...
by GitHub 02 Nov '15
by GitHub 02 Nov '15
02 Nov '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8b630d6d6c121659c1f93f9b51df8ccc8871b83a
https://github.com/galaxyproject/galaxy/commit/8b630d6d6c121659c1f93f9b51df…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
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
Log Message:
-----------
Update galaxy.jobs.runners.util from pulsar.managers.util
Commit: c46c7e082768ecd1c11fe20d3639ee5ada0ab61b
https://github.com/galaxyproject/galaxy/commit/c46c7e082768ecd1c11fe20d3639…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
A .ci/flake8_blacklist.txt
A .ci/flake8_wrapper.sh
M .gitignore
A .travis.yml
A CODE_OF_CONDUCT.md
M CONTRIBUTING.md
A CONTRIBUTORS.md
M LICENSE.txt
M README.rst
M client/GruntFile.js
A client/README.md
R client/README.txt
M client/bower.json
M client/galaxy/scripts/base.js
M client/galaxy/scripts/galaxy-app-base.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.masthead.js
M client/galaxy/scripts/galaxy.menu.js
M client/galaxy/scripts/galaxy.panels.js
R client/galaxy/scripts/galaxy.workflow_editor.canvas.js
R client/galaxy/scripts/galaxy.workflows.js
M client/galaxy/scripts/libs/backbone/backbone.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/jquery/jquery.js
R client/galaxy/scripts/libs/lunr.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/citation/citation-view.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
A client/galaxy/scripts/mvc/collection/collection-panel-edit.js
M client/galaxy/scripts/mvc/collection/collection-panel.js
A client/galaxy/scripts/mvc/collection/list-collection-creator.js
A client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
A client/galaxy/scripts/mvc/collection/pair-collection-creator.js
R client/galaxy/scripts/mvc/collection/paired-collection-creator.js
M client/galaxy/scripts/mvc/data.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-model.js
A client/galaxy/scripts/mvc/form/form-data.js
A client/galaxy/scripts/mvc/form/form-input.js
A client/galaxy/scripts/mvc/form/form-parameters.js
A client/galaxy/scripts/mvc/form/form-repeat.js
A client/galaxy/scripts/mvc/form/form-section.js
A client/galaxy/scripts/mvc/form/form-select-content.js
A 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-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-panel-annotated.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/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-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-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/tools.js
R client/galaxy/scripts/mvc/tools/tools-content.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
R client/galaxy/scripts/mvc/tools/tools-input.js
M client/galaxy/scripts/mvc/tools/tools-jobs.js
R client/galaxy/scripts/mvc/tools/tools-parameters.js
R client/galaxy/scripts/mvc/tools/tools-repeat.js
R client/galaxy/scripts/mvc/tools/tools-section.js
R client/galaxy/scripts/mvc/tools/tools-select-content.js
M client/galaxy/scripts/mvc/tools/tools-template.js
R client/galaxy/scripts/mvc/tools/tools-tree.js
A client/galaxy/scripts/mvc/ui/error-modal.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-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
A client/galaxy/scripts/mvc/ui/ui-list.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-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
A client/galaxy/scripts/mvc/ui/ui-select-ftp.js
A 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
A client/galaxy/scripts/mvc/workflow/workflow-canvas.js
A client/galaxy/scripts/mvc/workflow/workflow-connector.js
A client/galaxy/scripts/mvc/workflow/workflow-manager.js
A client/galaxy/scripts/mvc/workflow/workflow-node.js
A client/galaxy/scripts/mvc/workflow/workflow-terminals.js
A client/galaxy/scripts/mvc/workflow/workflow-view-data.js
A client/galaxy/scripts/mvc/workflow/workflow-view-node.js
A client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
A client/galaxy/scripts/mvc/workflow/workflow-view.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/templates/tool_search.handlebars
A client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/deferred.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/circster.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
A client/galaxy/style/blue_colors.ini
A client/galaxy/style/less/autocomplete_tagging.less
A client/galaxy/style/less/base.less
A client/galaxy/style/less/bootstrap.less
A client/galaxy/style/less/bootstrap/alerts.less
A client/galaxy/style/less/bootstrap/badges.less
A client/galaxy/style/less/bootstrap/bootstrap.less
A client/galaxy/style/less/bootstrap/breadcrumbs.less
A client/galaxy/style/less/bootstrap/button-groups.less
A client/galaxy/style/less/bootstrap/buttons.less
A client/galaxy/style/less/bootstrap/carousel.less
A client/galaxy/style/less/bootstrap/close.less
A client/galaxy/style/less/bootstrap/code.less
A client/galaxy/style/less/bootstrap/component-animations.less
A client/galaxy/style/less/bootstrap/dropdowns.less
A client/galaxy/style/less/bootstrap/forms.less
A client/galaxy/style/less/bootstrap/glyphicons.less
A client/galaxy/style/less/bootstrap/grid.less
A client/galaxy/style/less/bootstrap/input-groups.less
A client/galaxy/style/less/bootstrap/jumbotron.less
A client/galaxy/style/less/bootstrap/labels.less
A client/galaxy/style/less/bootstrap/list-group.less
A client/galaxy/style/less/bootstrap/media.less
A client/galaxy/style/less/bootstrap/mixins.less
A client/galaxy/style/less/bootstrap/modals.less
A client/galaxy/style/less/bootstrap/navbar.less
A client/galaxy/style/less/bootstrap/navs.less
A client/galaxy/style/less/bootstrap/normalize.less
A client/galaxy/style/less/bootstrap/pager.less
A client/galaxy/style/less/bootstrap/pagination.less
A client/galaxy/style/less/bootstrap/panels.less
A client/galaxy/style/less/bootstrap/popovers.less
A client/galaxy/style/less/bootstrap/print.less
A client/galaxy/style/less/bootstrap/progress-bars.less
A client/galaxy/style/less/bootstrap/responsive-utilities.less
A client/galaxy/style/less/bootstrap/scaffolding.less
A client/galaxy/style/less/bootstrap/tables.less
A client/galaxy/style/less/bootstrap/theme.less
A client/galaxy/style/less/bootstrap/thumbnails.less
A client/galaxy/style/less/bootstrap/tooltip.less
A client/galaxy/style/less/bootstrap/type.less
A client/galaxy/style/less/bootstrap/utilities.less
A client/galaxy/style/less/bootstrap/variables.less
A client/galaxy/style/less/bootstrap/wells.less
A client/galaxy/style/less/circster.less
A client/galaxy/style/less/collections.less
A client/galaxy/style/less/embed_item.less
A client/galaxy/style/less/fontawesome/bordered-pulled.less
A client/galaxy/style/less/fontawesome/core.less
A client/galaxy/style/less/fontawesome/fixed-width.less
A client/galaxy/style/less/fontawesome/font-awesome.less
A client/galaxy/style/less/fontawesome/icons.less
A client/galaxy/style/less/fontawesome/larger.less
A client/galaxy/style/less/fontawesome/list.less
A client/galaxy/style/less/fontawesome/mixins.less
A client/galaxy/style/less/fontawesome/path.less
A client/galaxy/style/less/fontawesome/rotated-flipped.less
A client/galaxy/style/less/fontawesome/spinning.less
A client/galaxy/style/less/fontawesome/stacked.less
A client/galaxy/style/less/fontawesome/variables.less
A client/galaxy/style/less/frame.less
A client/galaxy/style/less/galaxy_bootstrap.less
A client/galaxy/style/less/galaxy_bootstrap/overrides.less
A client/galaxy/style/less/galaxy_bootstrap/variables.less
A client/galaxy/style/less/galaxy_variables.less
A client/galaxy/style/less/history.less
A client/galaxy/style/less/iconic_stroke.less
A client/galaxy/style/less/iphone.less
A client/galaxy/style/less/job.less
A client/galaxy/style/less/jstree.less
A client/galaxy/style/less/library.less
A client/galaxy/style/less/list-item.less
A client/galaxy/style/less/masthead.less
A client/galaxy/style/less/reports.less
A client/galaxy/style/less/select2.less
A client/galaxy/style/less/theme/blue.less
A client/galaxy/style/less/toastr.less
A client/galaxy/style/less/trackster.less
A client/galaxy/style/less/ui.less
A client/galaxy/style/less/ui/dataset-choice.less
A client/galaxy/style/less/ui/icon-btn.less
A client/galaxy/style/less/ui/pagination.less
A client/galaxy/style/less/ui/paired-collection-creator.less
A client/galaxy/style/less/ui/peek-column-selector.less
A client/galaxy/style/less/ui/search-input.less
A client/galaxy/style/less/upload.less
A client/galaxy/style/source_material/circle.py
A client/galaxy/style/source_material/galaxy_icons.svg
A client/galaxy/style/source_material/galaxy_spinner.fla
A client/grunt-tasks/install-libs.js
A client/grunt-tasks/scripts.js
A client/grunt-tasks/style.js
A client/grunt-tasks/templates.js
M client/package.json
A client/toolshed/scripts/mvc/groups/group-detail-view.js
A client/toolshed/scripts/mvc/groups/group-list-view.js
A client/toolshed/scripts/mvc/groups/group-listrow-view.js
A client/toolshed/scripts/mvc/groups/group-model.js
A client/toolshed/scripts/toolshed.groups.js
A 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/object_store_conf.xml.sample
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/config/ipython.xml
M config/plugins/interactive_environments/ipython/templates/ipython.mako
M config/plugins/interactive_environments/ipython/templates/notebook.ipynb
A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
A config/plugins/interactive_environments/rstudio/config/rstudio.xml
A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/prng4.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rng.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rsa.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.min.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/jsbn.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/prng4.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rng.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rsa.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/jsbn.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/prng4.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rng.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rsa.js
A config/plugins/interactive_environments/rstudio/static/js/rstudio.js
A config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/visualizations/README.txt
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/static/build-app.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
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A config/plugins/visualizations/graphviz/templates/graphviz.mako
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M config/plugins/visualizations/sweepster/config/sweepster.xml
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M config/reports_wsgi.ini.sample
M config/tool_conf.xml.sample
M config/tool_data_table_conf.xml.sample
M config/tool_shed.ini.sample
M config/tool_sheds_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.py
M cron/parse_builds_3_sites.py
M display_applications/ensembl/ensembl_bam.xml
M display_applications/ensembl/ensembl_gff.xml
M display_applications/ensembl/ensembl_interval_as_bed.xml
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R eggs.ini
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M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
A lib/galaxy/auth/__init__.py
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M lib/galaxy/dataset_collections/builder.py
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M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/datatypes/assembly.py
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M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
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M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/ratable.py
A 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
A lib/galaxy/metadata
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
A 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/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/data_manager.py
M lib/galaxy/tools/actions/data_source.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/brew_util.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/modules.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/exception_handling.py
M lib/galaxy/tools/execute.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/lint.py
M lib/galaxy/tools/linters/citations.py
A lib/galaxy/tools/linters/command.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/input_translation.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/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/interface.py
A lib/galaxy/tools/parser/util.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/filters/__init__.py
A lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/lineages/stock.py
M lib/galaxy/tools/util/galaxyops/__init__.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
A 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/data_providers/registry.py
M lib/galaxy/visualization/genomes.py
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A lib/galaxy/visualization/plugins/config_parser.py
A lib/galaxy/visualization/plugins/plugin.py
A lib/galaxy/visualization/plugins/registry.py
A lib/galaxy/visualization/plugins/resource_parser.py
A lib/galaxy/visualization/plugins/utils.py
R lib/galaxy/visualization/registry.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/lib/proxy.js
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/authenticate.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/dataset_collections.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
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M lib/galaxy/webapps/galaxy/api/folder_contents.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/job_files.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/provenance.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.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/search.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
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M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
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R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
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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
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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
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M lib/galaxy/webapps/reports/controllers/jobs.py
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M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/system.py
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M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/__init__.py
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A lib/galaxy/webapps/tool_shed/api/configuration.py
A lib/galaxy/webapps/tool_shed/api/groups.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
R lib/galaxy/webapps/tool_shed/api/search.py
A lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/app.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
A 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
A 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/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/render.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/steps.py
A lib/galaxy_ext/__init__.py
A lib/galaxy_ext/metadata/__init__.py
A 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/transport/ssh.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
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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
A lib/tool_shed/managers/__init__.py
A lib/tool_shed/managers/groups.py
A lib/tool_shed/managers/repositories.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_tool_shed.sh
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_validator.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/tool_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/workflow_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
A scripts/binary_compatibility.py
A 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
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M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
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M scripts/data_libraries/build_whoosh_index.py
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M scripts/external_chown_script.py
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R scripts/scramble/scripts/pysam-solaris.py
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R static/images/SetAttr.png
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M static/scripts/utils/deferred.js
M static/scripts/utils/graph.js
M static/scripts/utils/levenshtein.js
M static/scripts/utils/localization.js
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M static/scripts/utils/natural-sort.js
A static/scripts/utils/query-string-parsing.js
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M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
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M static/scripts/viz/trackster/slotting.js
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M static/scripts/viz/visualization.js
M static/scripts/viz/viz_views.js
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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
A test/unit/datatypes/__init__.py
A test/unit/datatypes/dataproviders/__init__.py
R test/unit/datatypes/dataproviders/tempfilecache.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/test_command_factory.py
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
A test/unit/managers/__init__.py
A test/unit/managers/base.py
R test/unit/managers/mock.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
R test/unit/managers/test_ModelManager.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_data_parameters.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
A test/unit/unittest_utils/__init__.py
A test/unit/unittest_utils/galaxy_mock.py
A test/unit/unittest_utils/tempfilecache.py
A test/unit/unittest_utils/utility.py
R test/unit/util/utility.py
A test/unit/visualizations/__init__.py
A test/unit/visualizations/plugins/__init__.py
A test/unit/visualizations/plugins/test_VisualizationPlugin.py
A test/unit/visualizations/plugins/test_VisualizationsRegistry.py
R test/unit/visualizations/registry/test_VisualizationsRegistry.py
A test/unit/web/__init__.py
A test/unit/web/base/__init__.py
R test/unit/web/base/mock.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/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
M tool-data/shared/gbrowse/gbrowse_build_sites.txt
M tool-data/shared/igv/igv_build_sites.txt.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/access_libraries.xml
M tools/data_source/bed_convert.xml
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
M tools/data_source/eupathdb.xml
M tools/data_source/fly_modencode.xml
M tools/data_source/flymine.xml
M tools/data_source/flymine_test.xml
M tools/data_source/genbank.xml
M tools/data_source/import.xml
M tools/data_source/metabolicmine.xml
M tools/data_source/microbial_import.xml
M tools/data_source/modmine.xml
M tools/data_source/mousemine.xml
M tools/data_source/ratmine.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/data_source/upload.py
M tools/data_source/upload.xml
M tools/data_source/worm_modencode.xml
M tools/data_source/wormbase_test.xml
M tools/data_source/yeastmine.xml
M tools/data_source/zebrafishmine.xml
M tools/evolution/codingSnps.xml
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/CreateInterval.xml
M tools/filters/axt_to_concat_fasta.xml
M tools/filters/axt_to_fasta.xml
M tools/filters/axt_to_lav.xml
M tools/filters/axt_to_lav_code.py
M tools/filters/catWrapper.xml
M tools/filters/changeCase.xml
M tools/filters/commWrapper.xml
M tools/filters/condense_characters.xml
M tools/filters/convert_characters.xml
M tools/filters/cutWrapper.xml
M tools/filters/fileGrep.xml
M tools/filters/fixedValueColumn.xml
M tools/filters/gff/extract_GFF_Features.xml
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/gff/gtf_filter_by_attribute_values_list.xml
M tools/filters/gtf2bedgraph.xml
M tools/filters/headWrapper.xml
M tools/filters/joiner2.xml
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed.xml
M tools/filters/lav_to_bed_code.py
M tools/filters/pasteWrapper.xml
M tools/filters/remove_beginning.xml
M tools/filters/tailWrapper.xml
M tools/filters/ucsc_gene_bed_to_exon_bed.xml
M tools/filters/ucsc_gene_bed_to_intron_bed.xml
M tools/filters/ucsc_gene_table_to_intervals.xml
M tools/filters/uniq.py
M tools/filters/uniq.xml
M tools/filters/wc_gnu.xml
M tools/filters/wiggle_to_simple.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/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.py
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.xml
M tools/maf/maf_limit_to_species.xml
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.xml
M tools/maf/maf_thread_for_species.xml
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_fasta.xml
M tools/maf/maf_to_interval.xml
M tools/maf/vcf_to_maf_customtrack.xml
M tools/next_gen_conversion/solid2fastq.xml
M tools/phenotype_association/master2gd_snp.xml
M tools/phenotype_association/master2pg.xml
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/plotting/bar_chart.xml
M tools/plotting/boxplot.xml
M tools/solid_tools/maq_cs_wrapper_code.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/filtering.xml
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/stats/gsummary.xml
M tools/stats/gsummary.xml.groups
M tools/validation/fix_errors.xml
M tools/visualization/LAJ.xml
M tools/visualization/LAJ_code.py
A tox.ini
Log Message:
-----------
Merge branch 'dev' into pulsar-client-update
Commit: 1e2863dd1c7db1020ceba0a0cffb77c771c7e788
https://github.com/galaxyproject/galaxy/commit/1e2863dd1c7db1020ceba0a0cffb…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
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
A lib/galaxy/tools/linters/xsd.py
A lib/galaxy/tools/linters/xsd_util.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/util/xml_macros.py
Log Message:
-----------
Merge linting and tool loader changes from Planemo
Commit: 36eb1142c4c9bae876185d79f5d7229bf08c0b8d
https://github.com/galaxyproject/galaxy/commit/36eb1142c4c9bae876185d79f5d7…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
M lib/galaxy/tools/linters/tests.py
Log Message:
-----------
PEP-8 fix for linters
Commit: a9d79b34e65c914e569bc1713ee82dd8877c2d6f
https://github.com/galaxyproject/galaxy/commit/a9d79b34e65c914e569bc1713ee8…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
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
Log Message:
-----------
Merge Planemo and Galaxy tools.deps changes (and a PEP-8 fix)
Commit: 12fdd3f9d5758f8957d57591c4bbd777bd1d5723
https://github.com/galaxyproject/galaxy/commit/12fdd3f9d5758f8957d57591c4bb…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
Log Message:
-----------
Correct a mistakenly reformatted comment. Inline isn't possible because
hanging an inline violates E113 (although PEP-8 does not explicitly say
it's not allowed, but it does say "An inline comment is a comment on the
same line as a statement"), so convert the comments to block.
Commit: a1726d205d167a8eb30de427d56b81fdd7529397
https://github.com/galaxyproject/galaxy/commit/a1726d205d167a8eb30de427d56b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
Log Message:
-----------
Python 3-ify the object store (from Pulsar, for Planemo)
Commit: aefc35ae0309d7a9a4418cdf479821e07e154fbd
https://github.com/galaxyproject/galaxy/commit/aefc35ae0309d7a9a4418cdf4798…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-10-30 (Fri, 30 Oct 2015)
Changed paths:
R lib/galaxy/tools/linters/xsd.py
R lib/galaxy/tools/linters/xsd_util.py
Log Message:
-----------
Remove old XSD linting code.
Commit: 45e3257f04b3a3858f0a4f6298076d1f91acc712
https://github.com/galaxyproject/galaxy/commit/45e3257f04b3a3858f0a4f629807…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-10-30 (Fri, 30 Oct 2015)
Changed paths:
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
Log Message:
-----------
Restore changes to tool shed package resolver.
Commit: 4e9e9a17d1dfd322ffbcb2ecebc184fe5538ec7e
https://github.com/galaxyproject/galaxy/commit/4e9e9a17d1dfd322ffbcb2ecebc1…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-11-01 (Sun, 01 Nov 2015)
Changed paths:
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
R lib/galaxy/tools/linters/xsd.py
R lib/galaxy/tools/linters/xsd_util.py
Log Message:
-----------
Merge pull request #1 from jmchilton/pulsar-planemo-lib-update
Remove old XSD linting code.
Commit: 99319f59c88715e74290267d93018d1f172512ca
https://github.com/galaxyproject/galaxy/commit/99319f59c88715e74290267d9301…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-11-01 (Sun, 01 Nov 2015)
Changed paths:
M lib/galaxy/jobs/metrics/instrumenters/collectl.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/objectstore/__init__.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.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/util/xml_macros.py
Log Message:
-----------
Merge pull request #1005 from natefoo/pulsar-planemo-lib-update
Merge changes to common modules shared between Galaxy, Planemo, and Pulsar.
Compare: https://github.com/galaxyproject/galaxy/compare/cbc8c44f60b4...99319f59c887
1
0
[galaxyproject/galaxy] 602d05: Log TS installation commands with repository name
by GitHub 02 Nov '15
by GitHub 02 Nov '15
02 Nov '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 602d05408465bb69e2594d95c5a0d479bc7f5ce1
https://github.com/galaxyproject/galaxy/commit/602d05408465bb69e2594d95c5a0…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
Log Message:
-----------
Log TS installation commands with repository name
Fixes #436
Commit: 7813148d9a09198d1d00d4326403adf0aa1f2250
https://github.com/galaxyproject/galaxy/commit/7813148d9a09198d1d00d4326403…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2015-10-30 (Fri, 30 Oct 2015)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
Log Message:
-----------
Fix review comments
Commit: cbc8c44f60b45c8cefb0c34fa9abc9c5aa067af9
https://github.com/galaxyproject/galaxy/commit/cbc8c44f60b45c8cefb0c34fa9ab…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-11-01 (Sun, 01 Nov 2015)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
Log Message:
-----------
Merge pull request #1008 from erasche/installation_logging
Log TS installation commands with repository name
Compare: https://github.com/galaxyproject/galaxy/compare/f406cdefc79e...cbc8c44f60b4
1
0
02 Nov '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9c2a07d4242110642da7ca7f28eca772e8342acb
https://github.com/galaxyproject/galaxy/commit/9c2a07d4242110642da7ca7f28ec…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-10-26 (Mon, 26 Oct 2015)
Changed paths:
M .gitignore
Log Message:
-----------
Add run_framework_tests.html to .gitignore .
Commit: 3c7082c64a31fa8a0296d5655039ed772d4de3b0
https://github.com/galaxyproject/galaxy/commit/3c7082c64a31fa8a0296d5655039…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-10-26 (Mon, 26 Oct 2015)
Changed paths:
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
Log Message:
-----------
Fix doc/source/lib using "sphinx-apidoc -M -f -o doc/source/lib/ lib/"
Commit: 69cda4869051edce338e3e585345a500015b80ac
https://github.com/galaxyproject/galaxy/commit/69cda4869051edce338e3e585345…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-10-26 (Mon, 26 Oct 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/pulsar/client/transport/curl.py
M scripts/tools/maf/check_loc_file.py
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:
-----------
Remove remaining references to galaxy.eggs . flake8 some files in tools/ .
Commit: f406cdefc79e6ecf7801b7da0dd98dad9dc43955
https://github.com/galaxyproject/galaxy/commit/f406cdefc79e6ecf7801b7da0dd9…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-11-01 (Sun, 01 Nov 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M .gitignore
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/pulsar/client/transport/curl.py
M scripts/tools/maf/check_loc_file.py
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 pull request #990 from nsoranzo/post_eggs_smash
Remove remaining references to galaxy.eggs . flake8 some tools.
Compare: https://github.com/galaxyproject/galaxy/compare/d9d746675a60...f406cdefc79e
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bd95d7672d0cf9f164abd9bcb43485c946150fa7
https://github.com/galaxyproject/galaxy/commit/bd95d7672d0cf9f164abd9bcb434…
Author: James Taylor <james(a)jamestaylor.org>
Date: 2015-11-01 (Sun, 01 Nov 2015)
Changed paths:
M static/welcome.html.sample
Log Message:
-----------
Updates to default welcome page.
Reference CONTRIBUTORS.md, update institution references, update to
HTML5, use some standard classes for formatting, include links for
configuring and installling tools.
Commit: 12b6d43c81c2d1dadd24248ea329b662465633fb
https://github.com/galaxyproject/galaxy/commit/12b6d43c81c2d1dadd24248ea329…
Author: James Taylor <james(a)jamestaylor.org>
Date: 2015-11-01 (Sun, 01 Nov 2015)
Changed paths:
M client/galaxy/style/less/base.less
M static/style/blue/base.css
M static/welcome.html.sample
Log Message:
-----------
Change a.btn style, fix welcome link targets.
"a" elements styled with .btn will have no underline by default.
Commit: 2d60665ab503878731a4aacd8bd9873fc938281c
https://github.com/galaxyproject/galaxy/commit/2d60665ab503878731a4aacd8bd9…
Author: James Taylor <james(a)jamestaylor.org>
Date: 2015-11-01 (Sun, 01 Nov 2015)
Changed paths:
M static/welcome.html.sample
Log Message:
-----------
Fix link target in welcome
Commit: d9d746675a6072701197b2b3123b7eb51c3618f3
https://github.com/galaxyproject/galaxy/commit/d9d746675a6072701197b2b3123b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-11-01 (Sun, 01 Nov 2015)
Changed paths:
M client/galaxy/style/less/base.less
M static/style/blue/base.css
M static/welcome.html.sample
Log Message:
-----------
Merge pull request #1013 from jxtx/fix-default-welcome-references
Updates to default welcome page.
Compare: https://github.com/galaxyproject/galaxy/compare/6b0898c32785...d9d746675a60
1
0
[galaxyproject/galaxy] 4cbeba: Show masthead if login is required, add login page...
by GitHub 01 Nov '15
by GitHub 01 Nov '15
01 Nov '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4cbeba4d601d16755c334c713df44370c0553600
https://github.com/galaxyproject/galaxy/commit/4cbeba4d601d16755c334c713df4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-21 (Wed, 21 Oct 2015)
Changed paths:
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 lib/galaxy/managers/configuration.py
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/scripts/mvc/app/app-analysis.js
A static/scripts/mvc/app/app-login.js
M static/scripts/mvc/app/app-view.js
Log Message:
-----------
Show masthead if login is required, add login page to front end
Style fix
Commit: 66d3289b383e34093bf14c4dc3e696c9b66b6f48
https://github.com/galaxyproject/galaxy/commit/66d3289b383e34093bf14c4dc3e6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-21 (Wed, 21 Oct 2015)
Changed paths:
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/mvc/app/app-analysis.js
M client/galaxy/scripts/mvc/history/history-panel.js
M client/galaxy/scripts/mvc/history/multi-panel.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/style/less/library.less
M client/galaxy/style/less/list-item.less
M lib/galaxy/objectstore/s3.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/galaxy.library.js.map
M static/maps/mvc/app/app-analysis.js.map
M static/maps/mvc/history/history-panel.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-librarylist-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/list/list-panel.js.map
M static/scripts/galaxy.library.js
M static/scripts/mvc/app/app-analysis.js
M static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/history/multi-panel.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-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/list/list-panel.js
M static/style/blue/base.css
M static/style/blue/library.css
M templates/webapps/galaxy/root/index.mako
M tools/filters/cutWrapper.xml
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fix_require_login_003
Conflicts:
static/maps/mvc/app/app-analysis.js.map
static/scripts/mvc/app/app-analysis.js
Commit: 27bde1bb1de8bf0fbd873b7dc8db215235b2126e
https://github.com/galaxyproject/galaxy/commit/27bde1bb1de8bf0fbd873b7dc8db…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-28 (Wed, 28 Oct 2015)
Changed paths:
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/libs/jquery/jquery.dynatree.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/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/utils/deferred.js
M create_db.sh
R dist-eggs.ini
M doc/source/index.rst
A doc/source/project/issues.rst
R eggs.ini
M lib/galaxy/__init__.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.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/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.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/dataset.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/util/gff_util.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/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/pbs.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/managers/base.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/users.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/check.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/migrate/check.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/log/fluent_log.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/template.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/pluginframework.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/helpers/__init__.py
M lib/galaxy/web/framework/middleware/profile.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.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/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/tool_runner.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/buildapp.py
M 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/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/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.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/framework/middleware/hg.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/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/util.py
M lib/galaxy/workflow/render.py
M lib/galaxy_ext/metadata/set_metadata.py
R lib/pkg_resources.py
M lib/pulsar/client/config_util.py
M lib/pulsar/client/transport/poster.py
M lib/pulsar/client/transport/requests.py
M lib/tool_shed/capsule/capsule_manager.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/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/update_repository_manager.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 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/scripts/bootstrap_tool_shed/bootstrap_util.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/deprecate_repositories_without_metadata.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/hg_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 manage_db.sh
M manage_tools.sh
M requirements.txt
M run.sh
M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/api/common.py
A scripts/binary_compatibility.py
R scripts/check_eggs.py
M scripts/check_galaxy.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.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
R scripts/egg_packager_template.py
R scripts/fetch_eggs.py
M scripts/functional_tests.py
R scripts/make_egg_packager.py
M scripts/manage_db.py
M scripts/manage_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
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/summarize_timings.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 static/maps/galaxy.library.js.map
M static/maps/libs/jquery/jquery.dynatree.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/grid/grid-view.js.map
M static/maps/mvc/tools.js.map
M static/maps/mvc/tools/tools-form-base.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/maps/utils/deferred.js.map
M static/scripts/galaxy.library.js
M static/scripts/libs/jquery/jquery.dynatree.js
M static/scripts/mvc/app/app-analysis.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/tools.js
M static/scripts/mvc/tools/tools-form-base.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/utils/deferred.js
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
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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 templates/admin/requests/select_datasets_to_transfer.mako
M templates/admin/tool_shed_repository/common.mako
M templates/base/base_panels.mako
M templates/webapps/tool_shed/repository/common.mako
M test/base/instrument.py
M test/base/interactor.py
M test/base/nose_util.py
M test/base/test_db_util.py
M test/base/twilltestcase.py
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/functional/test_metadata_editing.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/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/tool_shed/base/test_db_util.py
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional_tests.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.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/tools/test_execution.py
M test/unit/workflows/test_modules.py
M tools/genomespace/genomespace_importer.xml
M tox.ini
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fix_require_login_003
Conflicts:
static/maps/mvc/app/app-analysis.js.map
static/scripts/mvc/app/app-analysis.js
Commit: f5a57b5f6ebf414fecfa2a6c325a5596fe11dd2b
https://github.com/galaxyproject/galaxy/commit/f5a57b5f6ebf414fecfa2a6c325a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Undo 965 for dev
Commit: bd383cc518f2f4335f3be97d50f33d66a081887f
https://github.com/galaxyproject/galaxy/commit/bd383cc518f2f4335f3be97d50f3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-10-29 (Thu, 29 Oct 2015)
Changed paths:
M static/maps/mvc/app/app-analysis.js.map
M static/scripts/mvc/app/app-analysis.js
Log Message:
-----------
Repack scripts
Commit: 6b0898c3278504f3bcac4493f7724b8e4862613e
https://github.com/galaxyproject/galaxy/commit/6b0898c3278504f3bcac4493f772…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-11-01 (Sun, 01 Nov 2015)
Changed paths:
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 lib/galaxy/managers/configuration.py
M lib/galaxy/web/framework/webapp.py
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/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
Log Message:
-----------
Merge pull request #968 from guerler/fix_require_login_003
Show masthead if login is required, add login page to front end
Compare: https://github.com/galaxyproject/galaxy/compare/c8c2f96b041a...6b0898c32785
1
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[galaxyproject/usegalaxy-playbook] 165139: include more info at the Main's homepage
by GitHub 01 Nov '15
by GitHub 01 Nov '15
01 Nov '15
Branch: refs/heads/martenson-patch-1
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 16513900e12388563df3d577c5a79c3fbc44e2bb
https://github.com/galaxyproject/usegalaxy-playbook/commit/16513900e1238856…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-11-01 (Sun, 01 Nov 2015)
Changed paths:
M templates/galaxy/common/static/welcome.html.j2
Log Message:
-----------
include more info at the Main's homepage
Please reword as proper but this message is really missing and I think we should highlight it as much as possible. This is a first step.
I have met so many people at #GI2015 that knew Galaxy but did not understand any of these two concepts and it would benefit them very much.
1
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