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December 2015
- 1 participants
- 195 discussions
Branch: refs/heads/revert-1222-release_15.10_tool_shed_fixes
Home: https://github.com/galaxyproject/galaxy
Commit: 1b9b05d40d1c50e37390740cbf6f6e50cf9db61d
https://github.com/galaxyproject/galaxy/commit/1b9b05d40d1c50e37390740cbf6f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml
Log Message:
-----------
Revert "[15.10] Tool Shed fixes."
1
0
[galaxyproject/galaxy] c9abc2: Fix for test/tool_shed/functional/test_1440_missin...
by GitHub 03 Dec '15
by GitHub 03 Dec '15
03 Dec '15
Branch: refs/heads/release_15.10
Home: https://github.com/galaxyproject/galaxy
Commit: c9abc2bc97dbdbe85c82946ca1138a6f6139bb33
https://github.com/galaxyproject/galaxy/commit/c9abc2bc97dbdbe85c82946ca113…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml
Log Message:
-----------
Fix for test/tool_shed/functional/test_1440_missing_env_sh_files.py .
Properly order the installation of the repositories adding
prior_installation_required="True". Otherwise filter_1440 is installed first
and ends in INSTALLED status because of the logic of
Repository.create_tool_dependency_with_initialized_env_sh_file() method
contained in
lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py .
Commit: 2b697e3c1ae76e4c718ed558e88a3c387d6e35c9
https://github.com/galaxyproject/galaxy/commit/2b697e3c1ae76e4c718ed558e88a…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
Fix detection of missing repository dependencies when reinstalling an updated Tool Shed repository.
Fix test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py .
Commit: 516b079ab97d7fc0a40255d03dcaf2cb600a2384
https://github.com/galaxyproject/galaxy/commit/516b079ab97d7fc0a40255d03dca…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml
Log Message:
-----------
Merge pull request #1222 from nsoranzo/release_15.10_tool_shed_fixes
[15.10] Tool Shed fixes.
Compare: https://github.com/galaxyproject/galaxy/compare/d1684e7c9d9d...516b079ab97d
1
0
[galaxyproject/infrastructure-playbook] 13c670: Packages for starforge builders
by GitHub 03 Dec '15
by GitHub 03 Dec '15
03 Dec '15
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: 13c6704efbd933deed082176f94d788d0abfa7a0
https://github.com/galaxyproject/infrastructure-playbook/commit/13c6704efbd…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M galaxyenv/group_vars/starforgebuilders.yml
Log Message:
-----------
Packages for starforge builders
Commit: fb562c67c2943d50d4178d2f04aa06ab5acb60c8
https://github.com/galaxyproject/infrastructure-playbook/commit/fb562c67c29…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M galaxyenv/host_vars/delirium.galaxyproject.org.yml
M galaxyenv/secret_group_vars/all.yml
A galaxyenv/secret_host_vars/delirium.galaxyproject.org.yml
M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml
Log Message:
-----------
Add a docs user to delirium for jenkins to update docs.galaxyproject.org
Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/8597fdb06f…
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: dd7bddcaa682d6d7cdaba8661c2c7cc80997ade0
https://github.com/galaxyproject/galaxy/commit/dd7bddcaa682d6d7cdaba8661c2c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Optimize initial queueing of jobs.
- Don't refresh job when this is the only thread fetching it.
- Avoid a bunch of unnecessary flushes, just flush once essentially during process.
Brings this process from taking over 1 second per job on average on sqlite for cat1 on my laptop to around 400 ms on average.
Commit: 299fbe99d7e157b9c01bbf0cdfcb7057dd59791a
https://github.com/galaxyproject/galaxy/commit/299fbe99d7e157b9c01bbf0cdfcb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Micro optimization, only fetch tool validation once per multi-run.
Commit: 876c28f88d81a8599a3278d9deac730adbac10d9
https://github.com/galaxyproject/galaxy/commit/876c28f88d81a8599a3278d9deac…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/execute.py
Log Message:
-----------
Add more job timers.
Commit: 41d3dc62f7e967ea3b409be410310563d0737bc4
https://github.com/galaxyproject/galaxy/commit/41d3dc62f7e967ea3b409be41031…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/collections.py
M lib/galaxy/model/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/execute.py
Log Message:
-----------
Parallelize executing tool parameter combinations.
Should work when mapping over collections or for big muli-run tool submissions.
Because of database tension with sqlalchemy it is not strictly a linear increase, but the end user walltime experience for a 24 dataset collection being submitted using 4 threads instead 1 drops execution time from 68 seconds to 35.
Rebased with fixes thanks to @nsoranzo - https://github.com/jmchilton/galaxy/commit/7f6514a21222ea787a0676764e4a4fe8….
Commit: 64b7cc9fef21caac5f9d21a8d42b60262fd28162
https://github.com/galaxyproject/galaxy/commit/64b7cc9fef21caac5f9d21a8d42b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
A test/functional/tools/create_10.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Add sample tool that creates 10 outputs.
Commit: a190b69e33a41717ddcc9eaa82826a82cc3d69b1
https://github.com/galaxyproject/galaxy/commit/a190b69e33a41717ddcc9eaa8282…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Optimize tools that produce multiple outputs.
Fetch HIDs for these datasets all at once and flush once for all assignments. Creating jobs from 4 threads each job producing 10 outputs - this resulted in reducing the runtime of this portion of the code by 90% and saving around 20 seconds per job.
Before:
galaxy.tools.actions INFO 2015-11-30 15:53:46,235 Add outputs to history (22494.829 ms)
galaxy.tools.actions INFO 2015-11-30 15:53:47,295 Add outputs to history (22239.062 ms)
galaxy.tools.actions INFO 2015-11-30 15:53:48,320 Add outputs to history (23781.079 ms)
galaxy.tools.actions INFO 2015-11-30 15:53:51,490 Add outputs to history (21820.567 ms)
galaxy.tools.actions INFO 2015-11-30 15:54:24,506 Add outputs to history (25353.837 ms)
After:
galaxy.tools.actions INFO 2015-11-30 16:08:47,640 Add outputs to history (2781.675 ms)
galaxy.tools.actions INFO 2015-11-30 16:08:47,860 Add outputs to history (3177.738 ms)
galaxy.tools.actions INFO 2015-11-30 16:08:48,776 Add outputs to history (2425.528 ms)
galaxy.tools.actions INFO 2015-11-30 16:09:02,942 Add outputs to history (2579.022 ms)
Commit: ab2c7c2c079b51ffd4ed7ef00724ef3f8d2636ec
https://github.com/galaxyproject/galaxy/commit/ab2c7c2c079b51ffd4ed7ef00724…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Tool execution micro optimization...
... Don't create an extra list to reverse, just iterate over in reversed order.
Commit: 9a1fc647a38007fef2a7a179648ea8f925ab5a8f
https://github.com/galaxyproject/galaxy/commit/9a1fc647a38007fef2a7a179648e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/managers/collections.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/execute.py
A test/functional/tools/create_10.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #1212 from jmchilton/tool_opts_6
Smaller Tool Optimization PR
Compare: https://github.com/galaxyproject/galaxy/compare/14ac3665ee37...9a1fc647a380
1
0
[galaxyproject/usegalaxy-playbook] 3f14df: $PATH is necessary. $VIRTUAL_ENV probably isn't.
by GitHub 03 Dec '15
by GitHub 03 Dec '15
03 Dec '15
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 3f14dfcddc36dc40c80222fe94d8b7678c7bb8bd
https://github.com/galaxyproject/usegalaxy-playbook/commit/3f14dfcddc36dc40…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M templates/supervisor/galaxy.conf.j2
Log Message:
-----------
$PATH is necessary. $VIRTUAL_ENV probably isn't.
1
0
[galaxyproject/galaxy] a5b7e6: Updated tool input collection to only add items fr...
by GitHub 03 Dec '15
by GitHub 03 Dec '15
03 Dec '15
Branch: refs/heads/release_15.10
Home: https://github.com/galaxyproject/galaxy
Commit: a5b7e6cb8e90387a7b9f6acb79b80a2114fa3928
https://github.com/galaxyproject/galaxy/commit/a5b7e6cb8e90387a7b9f6acb79b8…
Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this).
Commit: d1684e7c9d9dc42918004dc15bf1e7d039c96088
https://github.com/galaxyproject/galaxy/commit/d1684e7c9d9dc42918004dc15bf1…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Merge pull request #1224 from jmchilton/collection_naming_performance
[15.10] Backport #1217
Compare: https://github.com/galaxyproject/galaxy/compare/d83e8d358f1b...d1684e7c9d9d
1
0
03 Dec '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3374f948f4eba1a57a7fd863491545b082f56fa4
https://github.com/galaxyproject/galaxy/commit/3374f948f4eba1a57a7fd8634915…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-12 (Wed, 12 Aug 2015)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
Log Message:
-----------
Use asynchronous API calls for metadata reset.
Commit: 2bd158dcbd9633c6fc03ca28c19d63b5d33781fd
https://github.com/galaxyproject/galaxy/commit/2bd158dcbd9633c6fc03ca28c19d…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-12 (Wed, 12 Aug 2015)
Changed paths:
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
Log Message:
-----------
Minor cleanup.
Commit: bc22944326944f6de80b2f70650bf6020bfe1d21
https://github.com/galaxyproject/galaxy/commit/bc22944326944f6de80b2f70650b…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-12 (Wed, 12 Aug 2015)
Changed paths:
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
Log Message:
-----------
More cleanup.
Commit: c11c07d9bb124d41a301c5adf8f81c42b99430cc
https://github.com/galaxyproject/galaxy/commit/c11c07d9bb124d41a301c5adf8f8…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-11-25 (Wed, 25 Nov 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
M .gitignore
A CODE_OF_CONDUCT.md
M CONTRIBUTING.md
M CONTRIBUTORS.md
M README.rst
M client/GruntFile.js
M client/galaxy/scripts/galaxy-app-base.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
M client/galaxy/scripts/libs/jquery/jquery.dynatree.js
M client/galaxy/scripts/libs/jquery/select2.js
A client/galaxy/scripts/mvc/app/app-analysis.js
A client/galaxy/scripts/mvc/app/app-login.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-model.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-panel.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-list.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
A client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/history-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-edit-current.js
M client/galaxy/scripts/mvc/history/history-panel.js
M client/galaxy/scripts/mvc/history/history-structure-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/job/job-li.js
M client/galaxy/scripts/mvc/job/job-model.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/list/list-item.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/mvc/tags.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M client/galaxy/scripts/mvc/tools/tools-form-workflow.js
M client/galaxy/scripts/mvc/tools/tools-form.js
M client/galaxy/scripts/mvc/tools/tools-jobs.js
R client/galaxy/scripts/mvc/ui/ui-button-check.js
R client/galaxy/scripts/mvc/ui/ui-button-menu.js
A client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
A client/galaxy/scripts/mvc/upload/composite/composite-row.js
A client/galaxy/scripts/mvc/upload/composite/composite-view.js
A client/galaxy/scripts/mvc/upload/default/default-row.js
A client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
R client/galaxy/scripts/mvc/upload/upload-row.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/templates/compiled/tool_link.js
M client/galaxy/scripts/templates/tool_link.handlebars
M client/galaxy/scripts/utils/add-logging.js
M client/galaxy/scripts/utils/deferred.js
M client/galaxy/scripts/utils/metrics-logger.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/bootstrap.less
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/list-item.less
M client/galaxy/style/less/reports.less
M client/galaxy/style/less/trackster.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/grunt-tasks/scripts.js
M client/grunt-tasks/style.js
M client/package.json
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-listrow-view.js
M config/auth_conf.xml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml
A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M config/plugins/interactive_environments/ipython/static/js/ipython.js
M config/plugins/interactive_environments/ipython/templates/ipython.mako
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
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A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js
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M config/tool_data_table_conf.xml.sample
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A lib/galaxy/datatypes/constructive_solid_geometry.py
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M lib/galaxy/datatypes/converters/bgzip.py
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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
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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
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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
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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
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M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
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M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
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M lib/galaxy/model/migrate/versions/0126_password_reset.py
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M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/template.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/plugins/config_parser.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/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
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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/remoteuser.py
M lib/galaxy/web/framework/middleware/sentry.py
A lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
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M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.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/external_service.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
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M lib/galaxy/webapps/galaxy/controllers/mobile.py
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M lib/galaxy/webapps/galaxy/controllers/requests.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
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M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
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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/app.py
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M lib/galaxy/webapps/reports/controllers/query.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
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M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
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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
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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
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M lib/galaxy/webapps/tool_shed/security/__init__.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_ext/metadata/set_metadata.py
M lib/galaxy_utils/sequence/fasta.py
M lib/galaxy_utils/sequence/fastq.py
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M lib/galaxy_utils/sequence/vcf.py
R lib/pkg_resources.py
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M lib/pulsar/client/amqp_exchange.py
M lib/pulsar/client/amqp_exchange_factory.py
M lib/pulsar/client/client.py
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M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
A static/scripts/mvc/history/copy-dialog.js
M static/scripts/mvc/history/hda-li-edit.js
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M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-panel-edit-current.js
M static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/history/history-structure-view.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/job/job-li.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/library/library-folderlist-view.js
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M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/tools.js
M static/scripts/mvc/tools/tools-form-base.js
M static/scripts/mvc/tools/tools-form-workflow.js
M static/scripts/mvc/tools/tools-form.js
M static/scripts/mvc/tools/tools-jobs.js
R static/scripts/mvc/ui/ui-button-check.js
R static/scripts/mvc/ui/ui-button-menu.js
A static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-options.js
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M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
M static/scripts/mvc/upload/upload-row.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/mvc/user/user-model.js
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/templates/compiled/tool_link.js
M static/scripts/utils/add-logging.js
M static/scripts/utils/deferred.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/autocomplete_tagging.css
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M static/style/blue/iphone.css
M static/style/blue/library.css
M static/style/blue/reports.css
M static/style/blue/trackster.css
M static/welcome.html.sample
M templates/admin/reload_tool.mako
M templates/admin/requests/select_datasets_to_transfer.mako
M templates/admin/tool_shed_repository/common.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/galaxy_client_app.mako
M templates/page_base.mako
M templates/show_params.mako
M templates/spark_base.mako
M templates/user/login.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/admin/index.mako
R templates/webapps/galaxy/cloud/index.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/data_manager/view_job.mako
M templates/webapps/galaxy/galaxy.masthead.mako
A templates/webapps/galaxy/history/as_xml.mako
M templates/webapps/galaxy/history/copy.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/history/view_multiple.mako
R templates/webapps/galaxy/root/history.mako
R templates/webapps/galaxy/root/history_as_xml.mako
M templates/webapps/galaxy/root/index.mako
R templates/webapps/galaxy/root/tool_menu.mako
A templates/webapps/galaxy/root/tool_runner.mako
R templates/webapps/galaxy/tool_executed.mako
R templates/webapps/galaxy/tool_form.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/reports/job_info.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/registered_users_specified_date.mako
M templates/webapps/reports/registered_users_specified_month.mako
M templates/webapps/reports/requests_per_month_all.mako
M templates/webapps/reports/requests_per_user.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/reports/system.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
M templates/webapps/tool_shed/repository/common.mako
A test-data/1.RData
A test-data/3.bam
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M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
A test/api/workflows_format_2/README.txt
A test/api/workflows_format_2/__init__.py
A test/api/workflows_format_2/converter.py
A test/api/workflows_format_2/interface.py
A test/api/workflows_format_2/main.py
R test/api/yaml_to_workflow.py
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M test/base/instrument.py
M test/base/interactor.py
M test/base/nose_util.py
M test/base/test_data.py
M test/base/test_db_util.py
A test/base/test_logging.py
M test/base/tool_shed_util.py
M test/base/twilltestcase.py
M test/casperjs/anon-history-tests.js
M test/casperjs/api-hda-tests.js
M test/casperjs/api-history-tests.js
M test/casperjs/casperjs_runner.py
M test/casperjs/hda-state-tests.js
M test/casperjs/history-panel-tests.js
M test/casperjs/modules/historypanel.js
M test/casperjs/server_env.py
M test/docker/README.md
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/provision.yml
M test/docker/base/run_test_wrapper.sh
M test/docker/base/start_mysql.sh
M test/functional/test_metadata_editing.py
A test/functional/tools/cheetah_problem_syntax_error.xml
A test/functional/tools/cheetah_problem_unbound_var.xml
A test/functional/tools/cheetah_problem_unbound_var_input.xml
R test/functional/tools/compare_bam_as_sam.xml
M test/functional/tools/disambiguate_cond.xml
A test/functional/tools/maxseconds.xml
M test/functional/tools/metadata_bam.xml
M test/functional/tools/min_repeat.xml
M test/functional/tools/multi_data_param.xml
M test/functional/tools/multi_output_configured.xml
M test/functional/tools/output_format.xml
A test/functional/tools/output_format_collection.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/simple_constructs.yml
A test/functional/tools/unicode_stream.xml
M test/functional/tools/validation_repeat.xml
M test/install_and_test_tool_shed_repositories/base/test_db_util.py
M test/install_and_test_tool_shed_repositories/base/twilltestcase.py
M test/install_and_test_tool_shed_repositories/base/util.py
M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
M test/manual/workflows_scaling.py
M test/qunit/README.txt
M test/qunit/package.json
A test/qunit/test-app.js
M test/qunit/test-common.js
A test/qunit/test-data/bootstrapped.js
A test/qunit/test-data/fakeserver.js
M test/qunit/tests/galaxy-app-base.js
A test/qunit/tests/upload_dialog_tests.html
A test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/tool_shed/base/test_db_util.py
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_0000_basic_repository_features.py
M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_0020_basic_repository_dependencies.py
M test/tool_shed/functional/test_0030_repository_dependency_revisions.py
M test/tool_shed/functional/test_0040_repository_circular_dependencies.py
M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_0060_workflows.py
M test/tool_shed/functional/test_0070_invalid_tool.py
M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
M test/tool_shed/functional/test_0090_tool_search.py
M test/tool_shed/functional/test_0100_complex_repository_dependencies.py
M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_0130_datatype_converters.py
M test/tool_shed/functional/test_0140_tool_help_images.py
M test/tool_shed/functional/test_0150_prior_installation_required.py
M test/tool_shed/functional/test_0160_circular_prior_installation_required.py
M test/tool_shed/functional/test_0170_complex_prior_installation_required.py
M test/tool_shed/functional/test_0300_reset_all_metadata.py
M test/tool_shed/functional/test_0310_hg_push_from_api.py
M test/tool_shed/functional/test_0400_repository_component_reviews.py
M test/tool_shed/functional/test_0410_repository_component_review_access_control.py
M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
M test/tool_shed/functional/test_0430_browse_utilities.py
M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
M test/tool_shed/functional/test_0450_skip_tool_tests.py
M test/tool_shed/functional/test_0460_upload_to_repository.py
M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
M test/tool_shed/functional/test_0490_export_import_repositories.py
M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
M test/tool_shed/functional/test_0530_repository_admin_feature.py
M test/tool_shed/functional/test_1000_install_basic_repository.py
M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_1060_install_repository_with_workflow.py
M test/tool_shed/functional/test_1070_invalid_tool.py
M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
M test/tool_shed/functional/test_1085_repository_dependency_handling.py
M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py
M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py
M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
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M test/tool_shed/functional/test_1150_prior_installation_required.py
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M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
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M test/tool_shed/functional/test_1400_review_migration_stages.py
M test/tool_shed/functional/test_1410_update_manager.py
M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
M test/tool_shed/functional/test_1430_repair_installed_repository.py
M test/tool_shed/functional/test_1440_missing_env_sh_files.py
M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
M test/tool_shed/functional/test_1460_data_managers.py
M test/tool_shed/functional/test_1470_updating_installed_repositories.py
M test/tool_shed/functional_tests.py
M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_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/test_galaxy_mapping.py
M test/unit/test_objectstore.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/unittest_utils/utility.py
M test/unit/workflows/test_modules.py
R tool-data/fastx_clipper_sequences.txt
R tool-data/shared/ucsc/manual_builds.txt
A tool-data/shared/ucsc/manual_builds.txt.sample
M tools/data_source/biomart.xml
M tools/data_source/biomart_test.xml
M tools/data_source/data_source.py
R tools/data_source/echo.py
R tools/data_source/echo.xml
R tools/data_source/ucsc_archaea.xml
R tools/data_source/ucsc_filter.py
R tools/data_source/ucsc_proxy.py
R tools/data_source/ucsc_proxy.xml
M tools/data_source/ucsc_tablebrowser.xml
M tools/data_source/ucsc_tablebrowser_archaea.xml
M tools/data_source/ucsc_tablebrowser_test.xml
R tools/data_source/ucsc_testproxy.xml
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/extract/liftOver_wrapper.xml
M tools/filters/axt_to_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/cutWrapper.xml
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/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/wig_to_bigwig.xml
M tools/filters/wiggle_to_simple.py
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/interval2maf.py
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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/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/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ.xml
M tox.ini
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into async_metadata_reset
Commit: 14ac3665ee37224aa5278ce7a3876fb204b1bf2d
https://github.com/galaxyproject/galaxy/commit/14ac3665ee37224aa5278ce7a387…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
Log Message:
-----------
Merge pull request #598 from davebx/async_metadata_reset
Make bulk repository metadata resets asynchronous.
Compare: https://github.com/galaxyproject/galaxy/compare/92a7b995b05f...14ac3665ee37
1
0
[galaxyproject/galaxy] 362a25: Updated tool input collection to only add items fr...
by GitHub 03 Dec '15
by GitHub 03 Dec '15
03 Dec '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 362a25e6e6b03dfada43ad1b9ab651966936c795
https://github.com/galaxyproject/galaxy/commit/362a25e6e6b03dfada43ad1b9ab6…
Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this).
Commit: 92a7b995b05f7966e2936b62f052d3a4b8ed0642
https://github.com/galaxyproject/galaxy/commit/92a7b995b05f7966e2936b62f052…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Merge pull request #1217 from ericenns/collection-tool-input-fixes
Collection tool input mapping performance fixes
Compare: https://github.com/galaxyproject/galaxy/compare/a57095661246...92a7b995b05f
1
0
[galaxyproject/galaxy] aea04a: Added better support for formats that store triple...
by GitHub 03 Dec '15
by GitHub 03 Dec '15
03 Dec '15
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: aea04a98715d921eacf86d58ebf5fd754ecfcad1
https://github.com/galaxyproject/galaxy/commit/aea04a98715d921eacf86d58ebf5…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-06-24 (Wed, 24 Jun 2015)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/graph.py
A lib/galaxy/datatypes/triples.py
Log Message:
-----------
Added better support for formats that store triples, these formats include 'N-Triples', 'N3','Turtle','RDF/XML' and 'JSON-LD'
Commit: e097de3570cb525687ee1800c1582375c6e22b94
https://github.com/galaxyproject/galaxy/commit/e097de3570cb525687ee1800c158…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-06-24 (Wed, 24 Jun 2015)
Changed paths:
M .ci/pep8_sources.txt
M lib/galaxy/datatypes/triples.py
Log Message:
-----------
PEP-8 fixes for triples.py and to flake checks.
Commit: e714759d409a3099ba04284de8167f66af32424e
https://github.com/galaxyproject/galaxy/commit/e714759d409a3099ba04284de816…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-06-24 (Wed, 24 Jun 2015)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/graph.py
Log Message:
-----------
Add restore as deprecated old path to RDF.
It will be in many old datatype_conf.xml files so perhaps it should be deprecated before removing it completely. Using this new infrastructure - people will be warned if the they load it from the old location and told to update datatypes_conf.xml to reference the new location.
Commit: c9e27c9425932573d7c7503dedb655ef62a92914
https://github.com/galaxyproject/galaxy/commit/c9e27c9425932573d7c7503dedb6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-06-24 (Wed, 24 Jun 2015)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/triples.py
Log Message:
-----------
File reading infrastructure for datatypes.
Use to ensure triple-related datatypes properly close file handles and restrict the amount of memory they consume when reading lines from files.
Commit: 82f62bc14768e66fc1fb127058acd1c17e4ce3e1
https://github.com/galaxyproject/galaxy/commit/82f62bc14768e66fc1fb127058ac…
Author: Jesse <jesse.vandam(a)wur.nl>
Date: 2015-06-24 (Wed, 24 Jun 2015)
Changed paths:
M .ci/pep8_sources.txt
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/triples.py
Log Message:
-----------
Merge pull request #1 from jmchilton/triples
Various fixes for triples.py.
Commit: 6c3cedcfd517ac6af3c109a6eec2c555a8313d84
https://github.com/galaxyproject/galaxy/commit/6c3cedcfd517ac6af3c109a6eec2…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-06-24 (Wed, 24 Jun 2015)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
fix sniffers of the triple format
Commit: e5d1b4ee26a16d6f9859de0d1f5ee5b5113430c4
https://github.com/galaxyproject/galaxy/commit/e5d1b4ee26a16d6f9859de0d1f5e…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-06-24 (Wed, 24 Jun 2015)
Changed paths:
M lib/galaxy/datatypes/triples.py
Log Message:
-----------
fix comment in triples.py (example for regexp)
Commit: c03f84b1d76285f75d3b5f84c06e31fc5bf54f96
https://github.com/galaxyproject/galaxy/commit/c03f84b1d76285f75d3b5f84c06e…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-06-25 (Thu, 25 Jun 2015)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/triples.py
Log Message:
-----------
use sizehint from python readline(s) function for sniffers in triples.py
Commit: 94c00b0238d50d9703609000d25f6b1bc56a9281
https://github.com/galaxyproject/galaxy/commit/94c00b0238d50d9703609000d25f…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-06-25 (Thu, 25 Jun 2015)
Changed paths:
M lib/galaxy/datatypes/triples.py
Log Message:
-----------
PEP-8 fixes to triples.py
Commit: ae1a56e26d1931add633970a206b97aff3f45dae
https://github.com/galaxyproject/galaxy/commit/ae1a56e26d1931add633970a206b…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-06-26 (Fri, 26 Jun 2015)
Changed paths:
M lib/galaxy/datatypes/triples.py
Log Message:
-----------
Make the RDF sniffer in triples.py a bit more specific
Commit: fb2784003d39e7ae8ce144ff7ab793f65d4771d8
https://github.com/galaxyproject/galaxy/commit/fb2784003d39e7ae8ce144ff7ab7…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-08-24 (Mon, 24 Aug 2015)
Changed paths:
A .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
R .ci/pep8_sources.txt
M CONTRIBUTING.md
M client/GruntFile.js
M client/README.md
M client/bower.json
M client/galaxy/scripts/galaxy.menu.js
R client/galaxy/scripts/galaxy.workflow_editor.canvas.js
R client/galaxy/scripts/galaxy.workflows.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/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-panel-edit.js
M client/galaxy/scripts/mvc/history/history-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/list/list-panel.js
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M client/galaxy/scripts/mvc/tools/tools-form-workflow.js
M client/galaxy/scripts/mvc/ui/ui-button-menu.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
A client/galaxy/scripts/mvc/upload/composite/composite-row.js
A client/galaxy/scripts/mvc/upload/composite/composite-view.js
A client/galaxy/scripts/mvc/upload/default/default-row.js
A client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
R client/galaxy/scripts/mvc/upload/upload-row.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
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/utils/config.js
A client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/galaxy/style/less/history.less
A client/galaxy/style/less/reports.less
M client/galaxy/style/less/trackster.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/galaxy/style/source_material/circle.py
M client/grunt-tasks/install-libs.js
M client/grunt-tasks/scripts.js
M client/grunt-tasks/style.js
A client/grunt-tasks/templates.js
M client/package.json
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/object_store_conf.xml.sample
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M config/plugins/interactive_environments/ipython/templates/ipython.mako
M config/plugins/visualizations/charts/static/build-app.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/trackster/config/trackster.xml
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M doc/patch.py
A doc/source/api/guidelines.rst
A doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/index.rst
R doc/source/lib/fpconst.rst
M doc/source/lib/galaxy.actions.rst
A doc/source/lib/galaxy.auth.providers.rst
A doc/source/lib/galaxy.auth.rst
A doc/source/lib/galaxy.dataset_collections.rst
A doc/source/lib/galaxy.dataset_collections.types.rst
M doc/source/lib/galaxy.datatypes.converters.rst
A doc/source/lib/galaxy.datatypes.dataproviders.rst
M doc/source/lib/galaxy.datatypes.display_applications.rst
M doc/source/lib/galaxy.datatypes.rst
M doc/source/lib/galaxy.datatypes.util.rst
M doc/source/lib/galaxy.eggs.rst
M doc/source/lib/galaxy.exceptions.rst
M doc/source/lib/galaxy.external_services.result_handlers.rst
M doc/source/lib/galaxy.external_services.rst
M doc/source/lib/galaxy.forms.rst
M doc/source/lib/galaxy.jobs.actions.rst
M doc/source/lib/galaxy.jobs.deferred.rst
A doc/source/lib/galaxy.jobs.metrics.collectl.rst
A doc/source/lib/galaxy.jobs.metrics.instrumenters.rst
A doc/source/lib/galaxy.jobs.metrics.rst
M doc/source/lib/galaxy.jobs.rst
R doc/source/lib/galaxy.jobs.runners.cli_job.rst
R doc/source/lib/galaxy.jobs.runners.cli_shell.rst
A doc/source/lib/galaxy.jobs.runners.lwr_client.rst
A doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst
A doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst
M doc/source/lib/galaxy.jobs.runners.rst
A doc/source/lib/galaxy.jobs.runners.state_handlers.rst
A doc/source/lib/galaxy.jobs.runners.util.cli.job.rst
A doc/source/lib/galaxy.jobs.runners.util.cli.rst
A doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst
A doc/source/lib/galaxy.jobs.runners.util.condor.rst
A doc/source/lib/galaxy.jobs.runners.util.job_script.rst
A doc/source/lib/galaxy.jobs.runners.util.rst
M doc/source/lib/galaxy.jobs.splitters.rst
M doc/source/lib/galaxy.managers.rst
M doc/source/lib/galaxy.model.migrate.rst
R doc/source/lib/galaxy.model.orm.ext.rst
M doc/source/lib/galaxy.model.orm.rst
M doc/source/lib/galaxy.model.rst
A doc/source/lib/galaxy.model.tool_shed_install.migrate.rst
A doc/source/lib/galaxy.model.tool_shed_install.rst
M doc/source/lib/galaxy.objectstore.rst
M doc/source/lib/galaxy.openid.rst
M doc/source/lib/galaxy.quota.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.sample_tracking.rst
M doc/source/lib/galaxy.security.rst
M doc/source/lib/galaxy.tags.rst
R doc/source/lib/galaxy.tool_shed.migrate.rst
R doc/source/lib/galaxy.tool_shed.rst
R doc/source/lib/galaxy.tool_shed.tool_dependencies.rst
M doc/source/lib/galaxy.tools.actions.rst
M doc/source/lib/galaxy.tools.data.rst
A doc/source/lib/galaxy.tools.data_manager.rst
A doc/source/lib/galaxy.tools.deps.resolvers.rst
M doc/source/lib/galaxy.tools.deps.rst
A doc/source/lib/galaxy.tools.filters.rst
R doc/source/lib/galaxy.tools.genome_index.rst
M doc/source/lib/galaxy.tools.imp_exp.rst
A doc/source/lib/galaxy.tools.linters.rst
M doc/source/lib/galaxy.tools.parameters.rst
A doc/source/lib/galaxy.tools.parser.rst
M doc/source/lib/galaxy.tools.rst
M doc/source/lib/galaxy.tools.search.rst
A doc/source/lib/galaxy.tools.toolbox.filters.rst
A doc/source/lib/galaxy.tools.toolbox.lineages.rst
A doc/source/lib/galaxy.tools.toolbox.rst
M doc/source/lib/galaxy.tools.util.galaxyops.rst
M doc/source/lib/galaxy.tools.util.rst
M doc/source/lib/galaxy.util.backports.importlib.rst
M doc/source/lib/galaxy.util.backports.rst
A doc/source/lib/galaxy.util.log.rst
A doc/source/lib/galaxy.util.pastescript.rst
M doc/source/lib/galaxy.util.rst
M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst
M doc/source/lib/galaxy.visualization.data_providers.rst
M doc/source/lib/galaxy.visualization.genome.rst
A doc/source/lib/galaxy.visualization.plugins.rst
M doc/source/lib/galaxy.visualization.rst
M doc/source/lib/galaxy.visualization.tracks.rst
M doc/source/lib/galaxy.web.base.controllers.rst
M doc/source/lib/galaxy.web.base.rst
M doc/source/lib/galaxy.web.framework.helpers.rst
M doc/source/lib/galaxy.web.framework.middleware.rst
M doc/source/lib/galaxy.web.framework.rst
A doc/source/lib/galaxy.web.proxy.rst
M doc/source/lib/galaxy.web.rst
M doc/source/lib/galaxy.web.security.rst
R doc/source/lib/galaxy.webapps.community.controllers.rst
R doc/source/lib/galaxy.webapps.community.framework.middleware.rst
R doc/source/lib/galaxy.webapps.community.framework.rst
R doc/source/lib/galaxy.webapps.community.model.migrate.rst
R doc/source/lib/galaxy.webapps.community.model.rst
R doc/source/lib/galaxy.webapps.community.rst
R doc/source/lib/galaxy.webapps.community.security.rst
R doc/source/lib/galaxy.webapps.community.util.rst
M doc/source/lib/galaxy.webapps.galaxy.api.rst
M doc/source/lib/galaxy.webapps.galaxy.controllers.rst
M doc/source/lib/galaxy.webapps.galaxy.rst
M doc/source/lib/galaxy.webapps.reports.controllers.rst
M doc/source/lib/galaxy.webapps.reports.rst
M doc/source/lib/galaxy.webapps.rst
M doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst
M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst
M doc/source/lib/galaxy.webapps.tool_shed.framework.rst
M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst
M doc/source/lib/galaxy.webapps.tool_shed.model.rst
M doc/source/lib/galaxy.webapps.tool_shed.rst
A doc/source/lib/galaxy.webapps.tool_shed.search.rst
M doc/source/lib/galaxy.webapps.tool_shed.security.rst
M doc/source/lib/galaxy.webapps.tool_shed.util.rst
A doc/source/lib/galaxy.work.rst
M doc/source/lib/galaxy.workflow.rst
A doc/source/lib/galaxy.workflow.schedulers.rst
A doc/source/lib/galaxy_ext.metadata.rst
A doc/source/lib/galaxy_ext.rst
M doc/source/lib/galaxy_utils.rst
M doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/log_tempfile.rst
M doc/source/lib/mimeparse.rst
M doc/source/lib/modules.rst
M doc/source/lib/pkg_resources.rst
M doc/source/lib/psyco_full.rst
A doc/source/lib/pulsar.client.rst
A doc/source/lib/pulsar.client.staging.rst
A doc/source/lib/pulsar.client.transport.rst
A doc/source/lib/pulsar.rst
A doc/source/lib/tool_shed.capsule.rst
A doc/source/lib/tool_shed.dependencies.repository.rst
A doc/source/lib/tool_shed.dependencies.rst
A doc/source/lib/tool_shed.dependencies.tool.rst
A doc/source/lib/tool_shed.galaxy_install.datatypes.rst
M doc/source/lib/tool_shed.galaxy_install.grids.rst
A doc/source/lib/tool_shed.galaxy_install.metadata.rst
M doc/source/lib/tool_shed.galaxy_install.migrate.rst
A doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst
M doc/source/lib/tool_shed.galaxy_install.rst
A doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst
M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst
A doc/source/lib/tool_shed.galaxy_install.tools.rst
A doc/source/lib/tool_shed.galaxy_install.utility_containers.rst
M doc/source/lib/tool_shed.grids.rst
A doc/source/lib/tool_shed.managers.rst
A doc/source/lib/tool_shed.metadata.rst
A doc/source/lib/tool_shed.repository_types.rst
M doc/source/lib/tool_shed.rst
A doc/source/lib/tool_shed.tools.rst
M doc/source/lib/tool_shed.util.rst
A doc/source/lib/tool_shed.utility_containers.rst
M doc/source/project/organization.rst
M doc/source/releases/15.05.rst
M doc/source/releases/_header.rst
A doc/source/ts_api_doc.rst
M lib/galaxy/__init__.py
M lib/galaxy/actions/admin.py
M lib/galaxy/auth/providers/ldap_ad.py
A lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/chrominfo.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/coverage.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
A lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/eggs/__init__.py
M lib/galaxy/eggs/dist.py
M lib/galaxy/eggs/scramble.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/external_services/__init__.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/__init__.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/datasets.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/lwr.py
M lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handler_factory.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.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/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/0018_ordered_tags_and_page_tags.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/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.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/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/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.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/0053_item_ratings.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/0058_history_import_export.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/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.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/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.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/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/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.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/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/orm/__init__.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/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/quota/__init__.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/output.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/stock.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/sanitize_html.py
M lib/galaxy/util/specs.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/template.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/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
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/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/request_id.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/static.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/webapps/galaxy/api/annotations.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/extended_metadata.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/groups.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/item_tags.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/request_types.py
M lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
M lib/galaxy/webapps/galaxy/api/samples.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/biostar.py
R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
M lib/galaxy/webapps/galaxy/controllers/data_manager.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/error.py
M lib/galaxy/webapps/galaxy/controllers/external_service.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_admin.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/request_type.py
M lib/galaxy/webapps/galaxy/controllers/requests.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/__init__.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/reports/config.py
A lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/__init__.py
M lib/galaxy/webapps/tool_shed/api/authenticate.py
M lib/galaxy/webapps/tool_shed/api/categories.py
A lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/galaxy/webapps/tool_shed/model/migrate/check.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/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/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.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/0019_add_skip_tool_test_table_and_test_install_error_column.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/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/search/repo_search.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
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_ext/metadata/__init__.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/galaxy_utils/sequence/fasta.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/sequence.py
M lib/galaxy_utils/sequence/transform.py
M lib/galaxy_utils/sequence/vcf.py
M lib/log_tempfile.py
M lib/mimeparse.py
M lib/psyco_full.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/tool/tag_attribute_handler.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
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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/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/scripts/api/common.py
M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
M lib/tool_shed/scripts/check_repositories_for_functional_tests.py
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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/common_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
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M lib/tool_shed/util/tool_dependency_util.py
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M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M run_tests.sh
M scripts/api/common.py
A scripts/auth/pam_auth_helper.py
M scripts/bootstrap_history.py
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_eggs.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
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M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/db_shell.py
M scripts/dist-scramble.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/edam_mapping.py
M scripts/egg_packager_template.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/fetch_eggs.py
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M scripts/get_platforms.py
M scripts/helper.py
M scripts/make_egg_packager.py
M scripts/metagenomics/convert_title.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_table.py
M scripts/migrate_tools/migrate_tools.py
M scripts/nosetests.py
M scripts/paster.py
M scripts/runtime_stats.py
M scripts/scramble.py
M scripts/scramble/lib/scramble_lib.py
M scripts/scramble/scripts/DRMAA_python-macosx.py
M scripts/scramble/scripts/DRMAA_python-solaris.py
M scripts/scramble/scripts/DRMAA_python.py
M scripts/scramble/scripts/MySQL_python-solaris.py
M scripts/scramble/scripts/MySQL_python.py
M scripts/scramble/scripts/PyRods.py
M scripts/scramble/scripts/bx_python-solaris.py
M scripts/scramble/scripts/generic.py
M scripts/scramble/scripts/pbs_python.py
M scripts/scramble/scripts/psycopg2-linux.py
M scripts/scramble/scripts/psycopg2-macosx.py
M scripts/scramble/scripts/psycopg2-solaris.py
M scripts/scramble/scripts/psycopg2.py
M scripts/scramble/scripts/pysam-solaris.py
M scripts/scramble/scripts/pysqlite.py
M scripts/set_dataset_sizes.py
M scripts/set_metadata.py
M scripts/set_user_disk_usage.py
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/test_dist_egg.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M setup.cfg
R static/help.css
R static/help.html
R static/help.rst
R static/images/SetAttr.png
R static/images/SetGenome.png
R static/images/brochure.pdf
R static/images/galaxy.png
R static/images/galaxyLogo_small.png
R static/images/lock.jpg
R static/images/qk/quickie1_small.png
R static/images/qk/quickie2_small.png
R static/images/qk/quickie3_small.png
R static/images/qk/quickie4_small.png
R static/images/qk/quickie5_small.png
R static/images/qk/quickie6_small.png
R static/images/qk/quickie7_small.png
R static/images/screencast.png
R static/images/sequencer.png
R static/images/tools.gif
R static/images/toolsExpandingMenu.gif
R static/images/welcomePhoto.jpg
M static/maps/galaxy.interactive_environments.js.map
M static/maps/galaxy.menu.js.map
R static/maps/galaxy.workflow_editor.canvas.js.map
M static/maps/libs/d3.js.map
M static/maps/libs/farbtastic.js.map
M static/maps/libs/handlebars.runtime.js.map
A static/maps/libs/jquery.sparklines.js.map
M static/maps/libs/jquery/jqtouch.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/toastr.js.map
M static/maps/libs/tracekit.js.map
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/data.js.map
M static/maps/mvc/dataset/dataset-choice.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-panel-edit.js.map
M static/maps/mvc/history/history-panel.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/job/job-model.js.map
M static/maps/mvc/library/library-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/list/list-panel.js.map
M static/maps/mvc/tools.js.map
M static/maps/mvc/tools/tools-form-base.js.map
M static/maps/mvc/tools/tools-form-workflow.js.map
M static/maps/mvc/tools/tools-jobs.js.map
M static/maps/mvc/ui/ui-button-menu.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-popover.js.map
M static/maps/mvc/ui/ui-select-library.js.map
M static/maps/mvc/ui/ui-select.js.map
M static/maps/mvc/ui/ui-slider.js.map
A static/maps/mvc/upload/composite/composite-row.js.map
A static/maps/mvc/upload/composite/composite-view.js.map
A static/maps/mvc/upload/default/default-row.js.map
A static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-model.js.map
R static/maps/mvc/upload/upload-row.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/mvc/upload/upload-view.js.map
A static/maps/mvc/workflow/workflow-canvas.js.map
A static/maps/mvc/workflow/workflow-connector.js.map
A static/maps/mvc/workflow/workflow-manager.js.map
A static/maps/mvc/workflow/workflow-node.js.map
A static/maps/mvc/workflow/workflow-terminals.js.map
A static/maps/mvc/workflow/workflow-view-data.js.map
A static/maps/mvc/workflow/workflow-view-node.js.map
A static/maps/mvc/workflow/workflow-view-terminals.js.map
A static/maps/mvc/workflow/workflow-view.js.map
A static/maps/mvc/workflow/workflow.js.map
A static/maps/reports_webapp/run_stats.js.map
M static/maps/templates/compiled/panel_section.js.map
M static/maps/templates/compiled/tool_form.js.map
M static/maps/templates/compiled/tool_link.js.map
M static/maps/templates/compiled/tool_search.js.map
M static/maps/utils/config.js.map
M static/maps/utils/deferred.js.map
M static/maps/utils/graph.js.map
M static/maps/utils/metrics-logger.js.map
A static/maps/utils/query-string-parsing.js.map
M static/maps/utils/uploadbox.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/sweepster.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/filters.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/visualization.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/galaxy.menu.js
R static/scripts/galaxy.workflow_editor.canvas.js
M static/scripts/libs/d3.js
M static/scripts/libs/farbtastic.js
M static/scripts/libs/handlebars.runtime.js
A static/scripts/libs/jquery.sparklines.js
M static/scripts/libs/jquery/jqtouch.js
M static/scripts/libs/raven.js
M static/scripts/libs/require.js
M static/scripts/libs/toastr.js
M static/scripts/libs/tracekit.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/data.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-panel-edit.js
M static/scripts/mvc/history/history-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/list/list-panel.js
M static/scripts/mvc/tools.js
M static/scripts/mvc/tools/tools-form-base.js
M static/scripts/mvc/tools/tools-form-workflow.js
M static/scripts/mvc/tools/tools-jobs.js
M static/scripts/mvc/ui/ui-button-menu.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-select-library.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/mvc/ui/ui-slider.js
A static/scripts/mvc/upload/composite/composite-row.js
A static/scripts/mvc/upload/composite/composite-view.js
A static/scripts/mvc/upload/default/default-row.js
A static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
R static/scripts/mvc/upload/upload-row.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/upload/upload-view.js
A static/scripts/mvc/workflow/workflow-canvas.js
A static/scripts/mvc/workflow/workflow-connector.js
A static/scripts/mvc/workflow/workflow-manager.js
A static/scripts/mvc/workflow/workflow-node.js
A static/scripts/mvc/workflow/workflow-terminals.js
A static/scripts/mvc/workflow/workflow-view-data.js
A static/scripts/mvc/workflow/workflow-view-node.js
A static/scripts/mvc/workflow/workflow-view-terminals.js
A static/scripts/mvc/workflow/workflow-view.js
A static/scripts/mvc/workflow/workflow.js
A static/scripts/reports_webapp/run_stats.js
R static/scripts/templates/compile_templates.py
M static/scripts/templates/compiled/panel_section.js
M static/scripts/templates/compiled/tool_form.js
M static/scripts/templates/compiled/tool_link.js
M static/scripts/templates/compiled/tool_search.js
R static/scripts/templates/panel_section.handlebars
R static/scripts/templates/tool_form.handlebars
R static/scripts/templates/tool_link.handlebars
R static/scripts/templates/tool_search.handlebars
M static/scripts/utils/config.js
M static/scripts/utils/deferred.js
M static/scripts/utils/graph.js
M static/scripts/utils/metrics-logger.js
A static/scripts/utils/query-string-parsing.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M static/style/blue/autocomplete_tagging.css
M static/style/blue/base.css
M static/style/blue/circster.css
M static/style/blue/embed_item.css
M static/style/blue/iphone.css
M static/style/blue/library.css
M static/style/blue/masthead.css
A static/style/blue/reports.css
M static/style/blue/sprite-fugue.png
M static/style/blue/sprite-history-buttons.png
M static/style/blue/sprite-history-states.png
M static/style/blue/trackster.css
R static/welcome.rst
M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
M templates/base.mako
M templates/display_base.mako
A templates/page_base.mako
M templates/search/index.mako
M templates/show_params.mako
M templates/sorting_base.mako
A templates/spark_base.mako
M templates/tagging_common.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/sanitize_whitelist.mako
R templates/webapps/galaxy/cloud/index.mako
A templates/webapps/galaxy/history/as_xml.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/history/structure.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/library/common/ldda_info.mako
M templates/webapps/galaxy/library/common/ldda_permissions.mako
R templates/webapps/galaxy/root/history.mako
R templates/webapps/galaxy/root/history_as_xml.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/galaxy/workflow/editor_tool_form.mako
M templates/webapps/reports/base_panels.mako
M templates/webapps/reports/index.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/registered_users_specified_month.mako
M templates/webapps/reports/requests_per_month_all.mako
M templates/webapps/reports/requests_per_user.mako
M templates/webapps/reports/requests_user_per_month.mako
A templates/webapps/reports/run_stats.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
A templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
R templates/webapps/tool_shed/message.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_histories.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/yaml_to_workflow.py
M test/base/test_db_util.py
M test/base/twilltestcase.py
M test/casperjs/api-anon-history-permission-tests.js
M test/casperjs/api-history-permission-tests.js
M test/casperjs/hda-state-tests.js
M test/casperjs/modules/historypanel.js
M test/functional/test_admin_features.py
M test/functional/test_data_managers.py
M test/functional/test_data_security.py
M test/functional/test_get_data.py
M test/functional/test_library_features.py
M test/functional/test_library_security.py
M test/functional/test_library_templates.py
M test/functional/test_metadata_editing.py
M test/functional/test_sample_tracking.py
M test/functional/test_toolbox.py
M test/functional/test_ucsc_table_browser.py
M test/functional/test_user_info.py
A test/functional/tool-data/fasta_indexes.loc
M test/functional/tool-data/sample_tool_data_tables.xml
A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
A test/functional/tools/collection_creates_dynamic_nested.xml
A test/functional/tools/collection_creates_list_of_pairs.xml
A test/functional/tools/dbkey_filter_input.xml
A test/functional/tools/dbkey_filter_multi_input.xml
A test/functional/tools/environment_variables.xml
A test/functional/tools/output_collection_filter.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/workflow.py
M test/install_and_test_tool_shed_repositories/base/test_db_util.py
A test/qunit/test-app.js
M test/qunit/test-common.js
A test/qunit/test-data/bootstrapped.js
A test/qunit/test-data/fakeserver.js
A test/qunit/tests/upload_dialog_tests.html
A test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/tool_shed/base/test_db_util.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_rules/20_instance.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_objectstore.py
M test/unit/test_routes.py
M test/unit/test_sockets.py
M test/unit/tool_shed_unit_tests/test_fabric_util.py
M test/unit/tool_shed_unit_tests/test_td_common_util.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_parameter_parsing.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/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/workflows/test_extract_summary.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/srma_index.loc.sample
M tool_list.py
M tools/data_source/data_source.py
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/stats/grouping.py
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
Conflicts:
.ci/pep8_sources.txt
lib/galaxy/datatypes/graph.py
Commit: c873d565834b8aa9f5d39901e025bbcec5fa2631
https://github.com/galaxyproject/galaxy/commit/c873d565834b8aa9f5d39901e025…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-08-24 (Mon, 24 Aug 2015)
Changed paths:
M lib/galaxy/datatypes/graph.py
Log Message:
-----------
graph.RDF got defined twice after merge
Commit: ba054a189ef8efe922154c34462bf49d104d1abe
https://github.com/galaxyproject/galaxy/commit/ba054a189ef8efe922154c34462b…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-08-24 (Mon, 24 Aug 2015)
Changed paths:
M lib/galaxy/datatypes/graph.py
Log Message:
-----------
pip8 problem
Commit: 37f3bbf26772f78af132527a1aa19a8da60fb540
https://github.com/galaxyproject/galaxy/commit/37f3bbf26772f78af132527a1aa1…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-08-25 (Tue, 25 Aug 2015)
Changed paths:
M lib/galaxy/datatypes/triples.py
Log Message:
-----------
improved the specificity for the xml/rdf sniffer
Commit: 1444c101aaee74d5e6512a475295970973be68df
https://github.com/galaxyproject/galaxy/commit/1444c101aaee74d5e6512a475295…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-08-25 (Tue, 25 Aug 2015)
Changed paths:
M lib/galaxy/datatypes/triples.py
Log Message:
-----------
pip8 fix
Commit: 4203ab5b1f032d6f0bcda11295c2856171b738ce
https://github.com/galaxyproject/galaxy/commit/4203ab5b1f032d6f0bcda11295c2…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-08-25 (Tue, 25 Aug 2015)
Changed paths:
M lib/galaxy/datatypes/triples.py
Log Message:
-----------
fix
Commit: 00e58e21f93b0a13caacc23081e02ea4b140bf66
https://github.com/galaxyproject/galaxy/commit/00e58e21f93b0a13caacc23081e0…
Author: Jesse c j van Dam <jesse.vandam(a)wur.nl>
Date: 2015-10-19 (Mon, 19 Oct 2015)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
changed log.warn to print because log.warn will stop a job
Commit: a443d99fddc14b58698618860076032cb9540dca
https://github.com/galaxyproject/galaxy/commit/a443d99fddc14b58698618860076…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/graph.py
Log Message:
-----------
Undo deprecated datatypes stuff, doesn't work with Galaxy well.
Commit: 4c13c92540c7ed4f8305dcb0216c2a448f33c24d
https://github.com/galaxyproject/galaxy/commit/4c13c92540c7ed4f8305dcb0216c…
Author: Jesse <jesse.vandam(a)wur.nl>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/graph.py
Log Message:
-----------
Merge pull request #2 from jmchilton/triples_2
Remove deprecated datatype stuff
Commit: a57095661246fab1d9045e0cabb1845f662edb5d
https://github.com/galaxyproject/galaxy/commit/a57095661246fab1d9045e0cabb1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/graph.py
A lib/galaxy/datatypes/triples.py
Log Message:
-----------
Merge pull request #396 from jessevdam/dev
Added better support for formats that store triples.
Compare: https://github.com/galaxyproject/galaxy/compare/65e6a1c3b6ca...a57095661246
1
0
03 Dec '15
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: a733df0551b48378276c6c529b8262b8e5f18670
https://github.com/galaxyproject/usegalaxy-playbook/commit/a733df0551b48378…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-12-03 (Thu, 03 Dec 2015)
Changed paths:
M common_infrastructure.yml
M galaxy_infrastructure.yml
M templates/supervisor/galaxy.conf.j2
Log Message:
-----------
Set $VIRTUAL_ENV for handlers.
1
0