- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 562432: Add framework_py3 test target
by GitHub 16 Aug '18

16 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5624323a337a5d6176d3bb9be3bef599e65167b1 https://github.com/galaxyproject/galaxy/commit/5624323a337a5d6176d3bb9be3be… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: A .ci/jenkins/framework-py3/run_tests.sh M run_tests.sh Log Message: ----------- Add framework_py3 test target Commit: fc464f975878867ddc8ef90818db9faab31c7368 https://github.com/galaxyproject/galaxy/commit/fc464f975878867ddc8ef90818db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M test/functional/tools/metadata_biom1.xml Log Message: ----------- Allow 4 lines diff to acount for the prefix of python2 unicode strings Commit: 58067b4c896df7f2f48f3c7b6f4c92f9c6d6f265 https://github.com/galaxyproject/galaxy/commit/58067b4c896df7f2f48f3c7b6f4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix count_lines function for compressed datatypes that inherit from Text Commit: 79ec064214030badbc64694213db0ce4865b5e64 https://github.com/galaxyproject/galaxy/commit/79ec064214030badbc64694213db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- py3: Fix Biom1 datatype Commit: 37132212fe5e1fdf7f43e41c59eac051bfb8f389 https://github.com/galaxyproject/galaxy/commit/37132212fe5e1fdf7f43e41c59ea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/jobs/splitters/multi.py Log Message: ----------- py3: Fix file splitting for parallelism Commit: f831c616cb418f72baa1aae420b47a49a0aacc3c https://github.com/galaxyproject/galaxy/commit/f831c616cb418f72baa1aae420b4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- py3: fix paths_as_file functionality Commit: 70640071224745f61d756ed1475b5a03c85f4f40 https://github.com/galaxyproject/galaxy/commit/70640071224745f61d756ed1475b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Don't log error to provide arguments to __new__ for types that don't take arguments This is just very verbose and unneeded. Commit: ea0e3ffeb779fee900aa8dbc33773a921e39ec9c https://github.com/galaxyproject/galaxy/commit/ea0e3ffeb779fee900aa8dbc3377… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- py3: Fix dataset dataset collection Commit: a927413df22ff3454cf6c691f851cf54673eefb7 https://github.com/galaxyproject/galaxy/commit/a927413df22ff3454cf6c691f851… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M test/functional/tools/parallelism.xml M test/functional/tools/parallelism_optional.xml Log Message: ----------- Use exit code and quote file parameters for paralellism test tools Commit: b041e41155ac18252c46364ac409a9695d9f8bfb https://github.com/galaxyproject/galaxy/commit/b041e41155ac18252c46364ac409… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Write configfile in binary mode This fixes the unicode_stream tool on docker. Commit: 79decc3ba77c5fbcaf36a0cbb9aace16512bcf9d https://github.com/galaxyproject/galaxy/commit/79decc3ba77c5fbcaf36a0cbb9aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Use OrderedDict to collect implicit collections This should fix randomly failing tests that rely on the order of the implcit collection elements, like `test_map_over_two_collections_unlinked`. Commit: c430d4a6509375c5aaf658f149b3038aa8f34883 https://github.com/galaxyproject/galaxy/commit/c430d4a6509375c5aaf658f149b3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Fix selenium test setup Commit: 3957ed91e2d25faae9100c85bc19b9a1c5b3d68e https://github.com/galaxyproject/galaxy/commit/3957ed91e2d25faae9100c85bc19… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M templates/display_common.mako M templates/legacy/grid_base.mako M templates/tagging_common.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Fix errors found during selenium testing Commit: ae9effa61005504c51ca11adbbf6b70f95fab3b8 https://github.com/galaxyproject/galaxy/commit/ae9effa61005504c51ca11adbbf6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: A .ci/jenkins/selenium-py3/run_tests.sh Log Message: ----------- Add selenium py3 jenkins setup Commit: fb86e96bffecaef3861ce68db963c22aee193d54 https://github.com/galaxyproject/galaxy/commit/fb86e96bffecaef3861ce68db963… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Skip decoding to unicode strings in grids At this point we should not have bytestrings anymore (we might, but if we do we should fix that instead). Commit: 7559b90a692a72da2556c61b65c8615ddff822a5 https://github.com/galaxyproject/galaxy/commit/7559b90a692a72da2556c61b65c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/base/driver_util.py M test/functional/test_toolbox.py A test/functional/test_toolbox_pytest.py Log Message: ----------- Setup a simple pytest tool test Commit: d9f394793897a4429664027cbdaacbb8fca6d4e2 https://github.com/galaxyproject/galaxy/commit/d9f394793897a4429664027cbdaa… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: A .ci/jenkins/framework-py3/run_tests.sh A .ci/jenkins/selenium-py3/run_tests.sh M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/web/framework/helpers/grids.py M run_tests.sh M templates/display_common.mako M templates/legacy/grid_base.mako M templates/tagging_common.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/base/driver_util.py M test/functional/test_toolbox.py A test/functional/test_toolbox_pytest.py M test/functional/tools/metadata_biom1.xml M test/functional/tools/parallelism.xml M test/functional/tools/parallelism_optional.xml Log Message: ----------- Merge pull request #6605 from mvdbeek/enable_and_fix_framework_py3_test Enable and fix framework py3 tests Compare: https://github.com/galaxyproject/galaxy/compare/b9ca3b7c3396...d9f394793897 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] c6b593: Migrate API tests in test_jobs.py to use test_hist...
by GitHub 16 Aug '18

16 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c6b593b1ca6efa0ef60b1e9fdbed10022bf9fc4e https://github.com/galaxyproject/galaxy/commit/c6b593b1ca6efa0ef60b1e9fdbed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- Migrate API tests in test_jobs.py to use test_history context. More configurable, better error reporting, cleans up jobs, etc.. Commit: b9ca3b7c339628ac017ffc27a91659dce87c4a96 https://github.com/galaxyproject/galaxy/commit/b9ca3b7c339628ac017ffc27a916… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- Merge pull request #6593 from jmchilton/toward_test_history_cleaning Migrate API tests in test_jobs.py to use test_history context. Compare: https://github.com/galaxyproject/galaxy/compare/318fc0994903...b9ca3b7c3396 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 283947: Update ucsc genome-test server URL.
by GitHub 15 Aug '18

15 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 2839475967320b7d95ade125e542625c6d54c1b9 https://github.com/galaxyproject/galaxy/commit/2839475967320b7d95ade125e542… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Update ucsc genome-test server URL. Commit: 1cd36e3f815b6ad06da7a1aa1ee2c56d67edc36c https://github.com/galaxyproject/galaxy/commit/1cd36e3f815b6ad06da7a1aa1ee2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Bump version; 'patch' since it should be the exact same, as much as anything over the net ever could be\? Commit: 709e49f104e2cba5d180bffb0ed0fee175f5ffba https://github.com/galaxyproject/galaxy/commit/709e49f104e2cba5d180bffb0ed0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Merge pull request #6591 from dannon/ucsc-test-server-domain [18.05] Update UCSC genome-test server URLs Compare: https://github.com/galaxyproject/galaxy/compare/7e445be502a6...709e49f104e2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 5de98d: add trr datatype
by GitHub 15 Aug '18

15 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5de98d84709bceba887f040760763abf5500b096 https://github.com/galaxyproject/galaxy/commit/5de98d84709bceba887f04076076… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add trr datatype Commit: 0c2dc3aafb684fc13458ba682eb1c46fa6054d7e https://github.com/galaxyproject/galaxy/commit/0c2dc3aafb684fc13458ba682eb1… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: A lib/galaxy/datatypes/test/em.trr Log Message: ----------- add trr example file Commit: 572b9ced2dada0c5a99d52f6de3886ad85b9d368 https://github.com/galaxyproject/galaxy/commit/572b9ced2dada0c5a99d52f6de38… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- no edam format know yet Commit: e42829f03604c8ba0d4a467027c3c3eb689e8395 https://github.com/galaxyproject/galaxy/commit/e42829f03604c8ba0d4a467027c3… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- register datatype Commit: 318fc0994903d3598d9a62e1c8718cb7cde53bfe https://github.com/galaxyproject/galaxy/commit/318fc0994903d3598d9a62e1c871… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/em.trr Log Message: ----------- Merge pull request #6597 from bgruening/trr add trr datatype Compare: https://github.com/galaxyproject/galaxy/compare/ef0a51537e56...318fc0994903 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 3f032f: Rework and simplify data manager testing
by GitHub 15 Aug '18

15 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f032f6c383b108946f77f8fd6b7a02e98d474e1 https://github.com/galaxyproject/galaxy/commit/3f032f6c383b108946f77f8fd6b7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M scripts/functional_tests.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- Rework and simplify data manager testing We don't rely on TwillTestCase anymore, that is now exclusively used by ShedTwillTestCase. Then I've just re-used the infrastructure of ToolsTestCase for discovering tests, while making sure that we do use an admin API key during testing. Commit: e21d94298d5d215a0f4f31dae26848388c593590 https://github.com/galaxyproject/galaxy/commit/e21d94298d5d215a0f4f31dae268… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Look in self.tool_dir if repository_dir is not available Commit: ef0a51537e56e3257532df258494a00a8f7c2506 https://github.com/galaxyproject/galaxy/commit/ef0a51537e56e3257532df258494… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/verify/interactor.py M scripts/functional_tests.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- Merge pull request #6595 from mvdbeek/modernize_data_manager_testing_strip_twill Modernize data manager testing and strip twill Compare: https://github.com/galaxyproject/galaxy/compare/55756ba12de6...ef0a51537e56 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 6cbb57: Fix Location of Plugin Static Content
by GitHub 15 Aug '18

15 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 6cbb574553a882b7573d86f25bede17e7293cc76 https://github.com/galaxyproject/galaxy/commit/6cbb574553a882b7573d86f25bed… Author: Matthew Spelchak <mrs11teen(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- Fix Location of Plugin Static Content Commit: 7e445be502a64213c96cb233200aa0f53a2821f4 https://github.com/galaxyproject/galaxy/commit/7e445be502a64213c96cb233200a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- Merge pull request #6602 from phac-nml/ie_documentation_fix [18.05] Fix Location of Plugin Static Content In Documentation for 18.05 Compare: https://github.com/galaxyproject/galaxy/compare/1ddaf4a64d63...7e445be502a6 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] 0052c0: Fix CORS for InterMine
by GitHub 14 Aug '18

14 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0052c0badc0e3aaf69657b71ca4af78a927fb375 https://github.com/galaxyproject/usegalaxy-playbook/commit/0052c0badc0e3aaf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Fix CORS for InterMine **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 683ef6: Improve robustness of tour Selenium test.
by GitHub 14 Aug '18

14 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 683ef6eceea208c5c244bb9fe895b5e591dcb8df https://github.com/galaxyproject/galaxy/commit/683ef6eceea208c5c244bb9fe895… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Improve robustness of tour Selenium test. Give the URL upload jobs a bit more time to complete. https://github.com/galaxyproject/galaxy/issues/6581 might also improve this - I'm not sure. Commit: 55756ba12de6f40db077576d3bae961aea6f190d https://github.com/galaxyproject/galaxy/commit/55756ba12de6f40db077576d3bae… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #6582 from jmchilton/selenium_fixes_45 Improve robustness of tour Selenium test. Compare: https://github.com/galaxyproject/galaxy/compare/853b2d03abcf...55756ba12de6 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] 7386b9: Install cutadapt v1.16
by GitHub 14 Aug '18

14 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7386b956b04bd475479d557225ffc2d2c8873842 https://github.com/galaxyproject/usegalaxy-playbook/commit/7386b956b04bd475… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Install cutadapt v1.16 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] bd9213: Setup pytest python3 API testing
by GitHub 14 Aug '18

14 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd921368413002f6b57e0c6ee229b2ff06e7482d https://github.com/galaxyproject/galaxy/commit/bd921368413002f6b57e0c6ee229… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt A pytest.ini M run_tests.sh M scripts/plugin_staging.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Setup pytest python3 API testing Commit: 1b3f5550548741370e70ff2b25bc404e84d2594e https://github.com/galaxyproject/galaxy/commit/1b3f5550548741370e70ff2b25bc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Bump docker image version Commit: 7342a7ebbc404c275fb0635c1628eecb92b56ff5 https://github.com/galaxyproject/galaxy/commit/7342a7ebbc404c275fb0635c1628… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Avoid prepopulating database twice Commit: 4e3a981003f9bd0c99a604327e17f37e16f07f33 https://github.com/galaxyproject/galaxy/commit/4e3a981003f9bd0c99a604327e17… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Temporarily run tests with image published in my channel Commit: 661b3101c635fc376d9c16878fd8b23122ab4950 https://github.com/galaxyproject/galaxy/commit/661b3101c635fc376d9c16878fd8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: A .ci/jenkins/api-py3/run_tests.sh Log Message: ----------- Add py3 build script for jenkins Commit: 39e1877ccedd36242bc93696d897f62d5c8f0126 https://github.com/galaxyproject/galaxy/commit/39e1877ccedd36242bc93696d897… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Explicitly create a python 3 virtualenv Commit: 5b02f5ccedd87a9d529d19a49950df57cc29a8cf https://github.com/galaxyproject/galaxy/commit/5b02f5ccedd87a9d529d19a49950… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Bump docker image version Commit: eb1cb57f424d7ab286658699d2313621ed9e1d4e https://github.com/galaxyproject/galaxy/commit/eb1cb57f424d7ab286658699d231… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Fix up Dockerfile for bdbag installation Commit: 091ba0f32c75b6046938c95b0521b3271d9c3a72 https://github.com/galaxyproject/galaxy/commit/091ba0f32c75b6046938c95b0521… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Use 18.09.0 tag Commit: 327ec3d4e9e9d0ab15ae07c2cd0596d6a8abbe90 https://github.com/galaxyproject/galaxy/commit/327ec3d4e9e9d0ab15ae07c2cd05… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh Log Message: ----------- Do use python 3 Commit: a6b78e7a614aaf3e8254fdea32723f6f06678b5e https://github.com/galaxyproject/galaxy/commit/a6b78e7a614aaf3e8254fdea3272… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/base/populators.py Log Message: ----------- Decode bytestring returned by source_string Commit: d659d91d331eb434221940a1cddbd5458d75d8b3 https://github.com/galaxyproject/galaxy/commit/d659d91d331eb434221940a1cddb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/web/framework/middleware/batch.py Log Message: ----------- Decode body when using json.loads in batch middleware Commit: 61fa9711dc406dc15b434630aff3c3497f18fd52 https://github.com/galaxyproject/galaxy/commit/61fa9711dc406dc15b434630aff3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/base/populators.py M test/base/rules_test_data.py Log Message: ----------- More resource_string fixes Commit: 03f80f8aef781908f4290f613de9ee78f58b632c https://github.com/galaxyproject/galaxy/commit/03f80f8aef781908f4290f613de9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Patch LargeBinary to cast strings to bytestring I don't fully understand the issue, and we might be accumulating technical debt here. What I'm seeing without this commit is this when I run for instance the VisualizationsApiTestCase.test_create API test. ``` Traceback (most recent call last): File "/galaxy/lib/galaxy/web/framework/decorators.py", line 283, in decorator rval = func(self, trans, *args, **kwargs) File "/galaxy/lib/galaxy/webapps/galaxy/api/visualizations.py", line 55, in index visualizations = self.get_visualizations_by_user(trans, user) File "/galaxy/lib/galaxy/web/base/controller.py", line 664, in get_visualizations_by_user return query.all() File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/query.py", line 2737, in all return list(self) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 98, in instances util.raise_from_cause(err) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 187, in reraise raise value File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 79, in instances rows = [proc(row) for row in fetch] File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 79, in <listcomp> rows = [proc(row) for row in fetch] File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 493, in _instance loaded_instance, populate_existing, populators) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 604, in _populate_full populator(state, dict_, row) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/strategies.py", line 1782, in load_scalar_from_joined_new_row dict_[key] = _instance(row) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 493, in _instance loaded_instance, populate_existing, populators) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 593, in _populate_full dict_[key] = getter(row) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/sql/type_api.py", line 1204, in process return process_value(impl_processor(value), dialect) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/sql/sqltypes.py", line 902, in process value = bytes(value) TypeError: string argument without an encoding ``` I think LargeBinary isn't meant to store strings the way we do this (we dump JSON as bytestring), and somehow on python 3 we get unicode strings back from the database, which blows up here. I suspect this might be configured on the connection level (see http://docs.sqlalchemy.org/en/latest/dialects/postgresql.html#unicode) but not blowing up here seems like a good default. Commit: 2527038ffce1f7f1b987f9318671bc4fec567ec0 https://github.com/galaxyproject/galaxy/commit/2527038ffce1f7f1b987f9318671… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Mount in run_tests script at container runtime This allows changing variables in the script without rebuilding the container Commit: 3d9c0b154ab744345808d36c8af38972524ab2c3 https://github.com/galaxyproject/galaxy/commit/3d9c0b154ab744345808d36c8af3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/api/test_workflows.py M test/base/data/test_workflow_with_runtime_input.ga M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml Log Message: ----------- Make random_lines1 consistent on py2 and py3 (again) Turns out integers are used as is in `random.seed()`, but strings are hashed (in the version 1 protocol), and the hashing isn't stable. So instead we hack around this by using `ord()` on each character and concatenating the digits. Yucky, but probably better than using numpy and putting this tool on the list of tools that inherit galaxy's environment (or adding a requirement tag and resolving with conda ...). Commit: b2fed75059767aece3c0a75c630c9f30e31f0078 https://github.com/galaxyproject/galaxy/commit/b2fed75059767aece3c0a75c630c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-11 (Sat, 11 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Flip testing image back to galaxy namespace Commit: ae3d41924ac844d22c454fbd01d49a9ac3ee3b74 https://github.com/galaxyproject/galaxy/commit/ae3d41924ac844d22c454fbd01d4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/util/encoding_util.py Log Message: ----------- py3: Fix repository installation I'm very surprised this actually worked. I suppose we called my system's `hg` ?! Commit: 4d5ea3d724cf1a7fac1c6a2f9eeac133c47c2a06 https://github.com/galaxyproject/galaxy/commit/4d5ea3d724cf1a7fac1c6a2f9eea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: A .ci/jenkins/integration-py3/run_tests.sh M run_tests.sh Log Message: ----------- Start testing integration tests on python 3 Commit: b47c246e0c688be2f9474c36e1d12b786deb2ac0 https://github.com/galaxyproject/galaxy/commit/b47c246e0c688be2f9474c36e1d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix showing, creating and downloading HTML files Commit: 37b5120197d8a8bf39b52585408998252e601d82 https://github.com/galaxyproject/galaxy/commit/37b5120197d8a8bf39b525854089… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/renamed_temporary_file.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M test/integration/test_data_manager_table_reload.py M test/integration/tool_sheds_conf.xml M test/integration/uses_shed.py Log Message: ----------- py3: fix installing and running data managers Commit: 167e0e912907821943bd93eab2c0986a3d31136c https://github.com/galaxyproject/galaxy/commit/167e0e912907821943bd93eab2c0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Fix dictify_outputs The hack of setting `.__len` doesn't work on python 3. Subclassing OrderedDict and providing list-like access using integers should have the same effect. Commit: 14b1e1acd4eedce4a86b96094a496cbb76dd4239 https://github.com/galaxyproject/galaxy/commit/14b1e1acd4eedce4a86b96094a49… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/util/none_like.py Log Message: ----------- py3: Fix optional dataset bool value This fixes cheetah like `#if $input.dataset: ... #end if`. Which is a little weird, but fastqc uses this pattern. Commit: 344f68ea6d9c48a2a6f9dd56dd434633167d8f8e https://github.com/galaxyproject/galaxy/commit/344f68ea6d9c48a2a6f9dd56dd43… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M scripts/galaxy-main Log Message: ----------- py3: Fix uwsgi mule startup Commit: 0b30a94bbe34fb40eaf6fc97c816fcbe0586d078 https://github.com/galaxyproject/galaxy/commit/0b30a94bbe34fb40eaf6fc97c816… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- py3: Fix new direct API-backed uploads Commit: dc4a4b0eb5c9a07d9048e893b9fa48b43eb58c09 https://github.com/galaxyproject/galaxy/commit/dc4a4b0eb5c9a07d9048e893b9fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M scripts/secret_decoder_ring.py Log Message: ----------- py3: fix secret decoder script Commit: 293ce5a4720c7fc2ec26d44985750188e3762e6b https://github.com/galaxyproject/galaxy/commit/293ce5a4720c7fc2ec26d4498575… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M test/base/driver_util.py M test/integration/test_mules_as_job_handlers.py Log Message: ----------- py3: Fix mules test cases We're now just copying the current python path. Also the handler names have actually changed, I think this hasn't been updated after a late change (it is now as it should be, based on the documentation). Commit: cfce2468451e52c72bf7f0544c1bc7e209cc9224 https://github.com/galaxyproject/galaxy/commit/cfce2468451e52c72bf7f0544c1b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Fix GRT export test Commit: 620375c9d045e0085e2b260a97b3fdd5912fb45a https://github.com/galaxyproject/galaxy/commit/620375c9d045e0085e2b260a97b3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Do test mules on Jenkins, I don't see why this shouldn't work Commit: 6e7a66cdc0b9f467341af77d4d2fd5eadc9f409d https://github.com/galaxyproject/galaxy/commit/6e7a66cdc0b9f467341af77d4d2f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Fix repository dependency manager Commit: dd7e4c601a3f31ce9c4fa06afc8234a39f0a5804 https://github.com/galaxyproject/galaxy/commit/dd7e4c601a3f31ce9c4fa06afc82… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Deal with docker localhost quirks Commit: fc06e78743086d3078d18e3928512cf62915bfb9 https://github.com/galaxyproject/galaxy/commit/fc06e78743086d3078d18e392851… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- py3: Fix Maf datatype Commit: dfba132d11b0f6f6d15cb9fc8c79e0645640489e https://github.com/galaxyproject/galaxy/commit/dfba132d11b0f6f6d15cb9fc8c79… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/util/__init__.py Log Message: ----------- Fix stdout/stderr exception handling Commit: 853b2d03abcfe563b12c817db84d871fbc291725 https://github.com/galaxyproject/galaxy/commit/853b2d03abcfe563b12c817db84d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: A .ci/jenkins/api-py3/run_tests.sh A .ci/jenkins/integration-py3/run_tests.sh M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/__init__.py M lib/galaxy/util/none_like.py M lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/uploads.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/util/encoding_util.py A pytest.ini M run_tests.sh M scripts/galaxy-main M scripts/plugin_staging.py M scripts/secret_decoder_ring.py M test/api/test_workflows.py M test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py M test/base/populators.py M test/base/rules_test_data.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/integration/test_data_manager_table_reload.py M test/integration/test_mules_as_job_handlers.py M test/integration/test_scripts.py M test/integration/tool_sheds_conf.xml M test/integration/uses_shed.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml Log Message: ----------- Merge pull request #6565 from mvdbeek/setup_py3_test_job Setup py3 test job Compare: https://github.com/galaxyproject/galaxy/compare/164a7d7f04be...853b2d03abcf **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] dd5996: CORS header for InterMine on Test
by GitHub 14 Aug '18

14 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd5996384aba954e30f1c9a05d711b4813a6897c https://github.com/galaxyproject/usegalaxy-playbook/commit/dd5996384aba954e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- CORS header for InterMine on Test **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/usegalaxy-playbook] f96ac0: CORS header for InterMine on Test
by GitHub 14 Aug '18

14 Aug '18

Branch: refs/heads/swarmscale-2.0 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f96ac07e3c4319a8c1aa6d2a5036a4d080172488 https://github.com/galaxyproject/usegalaxy-playbook/commit/f96ac07e3c4319a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- CORS header for InterMine on Test **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] c2ab74: Add download option to workflow editor menu
by GitHub 14 Aug '18

14 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2ab74985148781f9a7eae16dec2fde89a0c154d https://github.com/galaxyproject/galaxy/commit/c2ab74985148781f9a7eae16dec2… Author: Anup Kumar <anup.rulez(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add download option to workflow editor menu Commit: 164a7d7f04be50e2ecd8edc64646a8e947680f4a https://github.com/galaxyproject/galaxy/commit/164a7d7f04be50e2ecd8edc64646… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6596 from bgruening/export_wf_galaxy_wf_editor Add download option to workflow editor menu Compare: https://github.com/galaxyproject/galaxy/compare/3d0763f71c79...164a7d7f04be **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 00e8d4: Quote Filter1 input and output
by GitHub 13 Aug '18

13 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 00e8d4ee76c65652e6a0b208f44d957c79db40b1 https://github.com/galaxyproject/galaxy/commit/00e8d4ee76c65652e6a0b208f44d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- Quote Filter1 input and output Commit: 819ee07af36d10734b32474fa832ce9e09e1b376 https://github.com/galaxyproject/galaxy/commit/819ee07af36d10734b32474fa832… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Respect unavilable peek when serializing HDA Also call display_peek() just once. That fixes the following exception that occurs when running the Filter1 tool through the API: ``` galaxy.datatypes.tabular ERROR 2018-08-12 22:53:42,939 make_html_peek_rows failed on HDA 64 Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/tabular.py", line 186, in make_html_peek_rows dataset.set_peek() File "/Users/mvandenb/src/galaxy/lib/galaxy/model/__init__.py", line 2264, in set_peek return self.datatype.set_peek(self) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/tabular.py", line 57, in set_peek super(TabularData, self).set_peek(dataset, line_count=line_count, WIDTH=WIDTH, skipchars=skipchars, line_wrap=False) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/data.py", line 813, in set_peek dataset.peek = get_file_peek(dataset.file_name, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/data.py", line 1029, in get_file_peek with compression_utils.get_fileobj(file_name, "U") as temp: File "/Users/mvandenb/src/galaxy/lib/galaxy/util/compression_utils.py", line 29, in get_fileobj return get_fileobj_raw(filename, mode, compressed_formats)[1] File "/Users/mvandenb/src/galaxy/lib/galaxy/util/compression_utils.py", line 58, in get_fileobj_raw return compressed_format, io.open(filename, mode, encoding='utf-8') FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpan_4qaow/tmpfzus9jhv/tmplqjtbp5c/database/files/000/dataset_40.dat' ``` This is because we serialize the HDA just after the job has been created, meaning the file may not exist yet. Commit: f4343d876f13e55e92ca228582b4430dcd01e4aa https://github.com/galaxyproject/galaxy/commit/f4343d876f13e55e92ca228582b4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Clarify set_peek setting when finishing job Commit: 3d0763f71c795549e6c133f2734cf7ae5337c296 https://github.com/galaxyproject/galaxy/commit/3d0763f71c795549e6c133f2734c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M tools/stats/filtering.xml Log Message: ----------- Merge pull request #6594 from mvdbeek/respect_unavailable_display_peek Respect unavailable display peek Compare: https://github.com/galaxyproject/galaxy/compare/e853762fdbb2...3d0763f71c79 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 07d415: Show workflow parameters in worklfow editor below ...
by GitHub 13 Aug '18

13 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07d41517460eedf514071cd1b66c7d958ad23037 https://github.com/galaxyproject/galaxy/commit/07d41517460eedf514071cd1b66c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Show workflow parameters in worklfow editor below title header Commit: 4550a7152c1be518effac678b807da9748b997eb https://github.com/galaxyproject/galaxy/commit/4550a7152c1be518effac678b807… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Workflow parameter positioning tweaks, keeps display to the right and minimally large. Commit: e853762fdbb20c7d9396223f17b2cd728d29dd68 https://github.com/galaxyproject/galaxy/commit/e853762fdbb20c7d9396223f17b2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6592 from guerler/fix_workflow_parameters Resolve overlap of workflow parameter container with gear-icon in editor header Compare: https://github.com/galaxyproject/galaxy/compare/0b1d804cf675...e853762fdbb2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] e3435e: Remove backbone thumbnail element
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e3435eb23d62815f5a08aca7dbaf68991b05ab60 https://github.com/galaxyproject/galaxy/commit/e3435eb23d62815f5a08aca7dbaf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: R client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/qunit/tests/ui_tests.js Log Message: ----------- Remove backbone thumbnail element Commit: 03702d0a61733682cd80ee3d4849cd094c00d0d1 https://github.com/galaxyproject/galaxy/commit/03702d0a61733682cd80ee3d4849… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove unused thumbnail styles Commit: 0b1d804cf675fb47f4132363f32b27680becbdf8 https://github.com/galaxyproject/galaxy/commit/0b1d804cf675fb47f4132363f32b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue R client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6587 from guerler/remove_bb_thumbnail Remove backbone version of thumbnail element Compare: https://github.com/galaxyproject/galaxy/compare/0ea1430136c5...0b1d804cf675 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 1d0f51: Fix upload file selector value resetting
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d0f51a05e5e5fb73940d7dae284bf9c00a4054c https://github.com/galaxyproject/galaxy/commit/1d0f51a05e5e5fb73940d7dae284… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix upload file selector value resetting Fix Commit: f992980d458edeebc0501ac036c2ee5c6fba7989 https://github.com/galaxyproject/galaxy/commit/f992980d458edeebc0501ac036c2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6573 from guerler/fix_upload_naming [18.05] Fix upload file selector value resetting Commit: ec60327f983ced46fa2a8489c359100960b72d5b https://github.com/galaxyproject/galaxy/commit/ec60327f983ced46fa2a8489c359… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Client rebuild to include uploadbox value fix in release branch. Commit: d7398672a1a3432ae11b0c41b291e45e77bbd183 https://github.com/galaxyproject/galaxy/commit/d7398672a1a3432ae11b0c41b291… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6574 from dannon/release_18.05 [18.05] Client rebuild to include uploadbox value fix in release branch. Commit: 2f87087ba2a88d71d539f888401d79167997a4ea https://github.com/galaxyproject/galaxy/commit/2f87087ba2a88d71d539f888401d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Use object store to check for existence of extra_files_path This should fix https://github.com/galaxyproject/galaxy/issues/6585 Commit: 1ddaf4a64d6307fd477653d3bba7353a30e88eb2 https://github.com/galaxyproject/galaxy/commit/1ddaf4a64d6307fd477653d3bba7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #6588 from mvdbeek/extra_path_nested_object_store_issue [18.05] Use object store to check for existence of extra_files_path Commit: 0ea1430136c51c5558f17e4a051e8d1a58009fd3 https://github.com/galaxyproject/galaxy/commit/0ea1430136c51c5558f17e4a051e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9910ea47d9b3...0ea1430136c5 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 2f8708: Use object store to check for existence of extra_f...
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 2f87087ba2a88d71d539f888401d79167997a4ea https://github.com/galaxyproject/galaxy/commit/2f87087ba2a88d71d539f888401d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Use object store to check for existence of extra_files_path This should fix https://github.com/galaxyproject/galaxy/issues/6585 Commit: 1ddaf4a64d6307fd477653d3bba7353a30e88eb2 https://github.com/galaxyproject/galaxy/commit/1ddaf4a64d6307fd477653d3bba7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #6588 from mvdbeek/extra_path_nested_object_store_issue [18.05] Use object store to check for existence of extra_files_path Compare: https://github.com/galaxyproject/galaxy/compare/d7398672a1a3...1ddaf4a64d63 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 4d1ce0: Cancel jobs when exiting test_history decorator.
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4d1ce0f431d337a45964eee3aa3813be1f4e41c6 https://github.com/galaxyproject/galaxy/commit/4d1ce0f431d337a45964eee3aa38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Cancel jobs when exiting test_history decorator. Should reduce the probability of a test interferring with other tests. Commit: 136255c0ad7a2aca6584f4c1fa3d10ea5e4a632e https://github.com/galaxyproject/galaxy/commit/136255c0ad7a2aca6584f4c1fa3d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M run_tests.sh M test/base/populators.py Log Message: ----------- Allow test_history context to annotate whether new histories are needed by test. Usually tests should have new histories but we should still capture this information so we can target tests are particular histories for debugging interactively and so we could potentially reduce the number of new histories created when testing remote Galaxies (there have been complaints about this in the past). Commit: 36e1d6cfce946b46f5904af3cc924cb0f21970ee https://github.com/galaxyproject/galaxy/commit/36e1d6cfce946b46f5904af3cc92… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M test/api/test_tools.py M test/base/populators.py Log Message: ----------- More use of test_history contextmanager in test_tools. Commit: 9910ea47d9b353fe61fc510469a0599210009a25 https://github.com/galaxyproject/galaxy/commit/9910ea47d9b353fe61fc510469a0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh M test/api/test_tools.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #6586 from jmchilton/toward_test_history_cleaning Smarter Test Histories (Part I) Compare: https://github.com/galaxyproject/galaxy/compare/5d85c32da243...9910ea47d9b3 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 38e581: Redirect unindentifed routes in admin panel
by GitHub 08 Aug '18

08 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38e5816b06d0804324dfe2a9c642859d990cfdb9 https://github.com/galaxyproject/galaxy/commit/38e5816b06d0804324dfe2a9c642… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-28 (Sat, 28 Jul 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Redirect unindentifed routes in admin panel Fix Commit: af755a098061f8db55db5ecc398c3410f180f9e1 https://github.com/galaxyproject/galaxy/commit/af755a098061f8db55db5ecc398c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Minor import cleanup, formatting. Commit: 4072d68e0d6d182a4249df143ab4fcba3e8f35cf https://github.com/galaxyproject/galaxy/commit/4072d68e0d6d182a4249df143ab4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js Log Message: ----------- Redirect without using backbone Commit: 5d85c32da24396a4853d09cf5fccb12481f1ccee https://github.com/galaxyproject/galaxy/commit/5d85c32da24396a4853d09cf5fcc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Merge pull request #6551 from guerler/fix_admin_routes Redirect unidentified routes in admin panel Compare: https://github.com/galaxyproject/galaxy/compare/75e50d3fdd98...5d85c32da243 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] c2246d: Fix last consistently failing Selenium test.
by GitHub 08 Aug '18

08 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2246d8b8a17fdf126aefb5f6b53eb680bb58848 https://github.com/galaxyproject/galaxy/commit/c2246d8b8a17fdf126aefb5f6b53… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/base/rules_test_data.py Log Message: ----------- Fix last consistently failing Selenium test. Commit: 75e50d3fdd98a75cc0c109616293608bdab5eac3 https://github.com/galaxyproject/galaxy/commit/75e50d3fdd98a75cc0c109616293… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/base/rules_test_data.py Log Message: ----------- Merge pull request #6578 from jmchilton/selenium_fixes_44 Fix last consistently failing Selenium test. Compare: https://github.com/galaxyproject/galaxy/compare/a7e159dd8b8c...75e50d3fdd98 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] ec6032: Client rebuild to include uploadbox value fix in r...
by GitHub 08 Aug '18

08 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: ec60327f983ced46fa2a8489c359100960b72d5b https://github.com/galaxyproject/galaxy/commit/ec60327f983ced46fa2a8489c359… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Client rebuild to include uploadbox value fix in release branch. Commit: d7398672a1a3432ae11b0c41b291e45e77bbd183 https://github.com/galaxyproject/galaxy/commit/d7398672a1a3432ae11b0c41b291… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6574 from dannon/release_18.05 [18.05] Client rebuild to include uploadbox value fix in release branch. Compare: https://github.com/galaxyproject/galaxy/compare/f992980d458e...d7398672a1a3 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 4f3cd8: Typo and wording fixes for dependency resolvers do...
by GitHub 07 Aug '18

07 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f3cd889f1cb2371519cabbc975dfffee6ec9b71 https://github.com/galaxyproject/galaxy/commit/4f3cd889f1cb2371519cabbc975d… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Typo and wording fixes for dependency resolvers docs Commit: a7e159dd8b8c584772defb6becb56f5450172dad https://github.com/galaxyproject/galaxy/commit/a7e159dd8b8c584772defb6becb5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Merge pull request #6575 from afgane/dev Typo and wording fixes for dependency resolvers docs Compare: https://github.com/galaxyproject/galaxy/compare/55436c38008c...a7e159dd8b8c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 1d0f51: Fix upload file selector value resetting
by GitHub 07 Aug '18

07 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 1d0f51a05e5e5fb73940d7dae284bf9c00a4054c https://github.com/galaxyproject/galaxy/commit/1d0f51a05e5e5fb73940d7dae284… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix upload file selector value resetting Fix Commit: f992980d458edeebc0501ac036c2ee5c6fba7989 https://github.com/galaxyproject/galaxy/commit/f992980d458edeebc0501ac036c2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6573 from guerler/fix_upload_naming [18.05] Fix upload file selector value resetting Compare: https://github.com/galaxyproject/galaxy/compare/ea085b07a0ef...f992980d458e **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] fa3a23: WIP: add a SelectTagParameter
by GitHub 07 Aug '18

07 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa3a2371e1b2873456a3034874036d9b8cadd01c https://github.com/galaxyproject/galaxy/commit/fa3a2371e1b2873456a303487403… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py Log Message: ----------- WIP: add a SelectTagParameter Commit: 4afbdbab31791101578be08acc3526e04c1835d6 https://github.com/galaxyproject/galaxy/commit/4afbdbab31791101578be08acc35… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M test/unit/test_objectstore.py M test/unit/tools/test_wrappers.py Log Message: ----------- Fix unit tests Commit: 04b0cfcc1388de18aeb93a39fa44451009bbd67f https://github.com/galaxyproject/galaxy/commit/04b0cfcc1388de18aeb93a39fa44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Make `get_datasets_for_group` case insensitive to tag Commit: 45b2b7f434fc1bd1e646c72c6024bacc482a8b8e https://github.com/galaxyproject/galaxy/commit/45b2b7f434fc1bd1e646c72c6024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DataDialog.vue A client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue A client/galaxy/scripts/components/Sharing.vue A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/DataTypes.vue R client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/communication-server-view.js A client/galaxy/scripts/layout/data.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/legacy/grid/grid-view.js R client/galaxy/scripts/libs/bootstrap-tour.js R client/galaxy/scripts/libs/bootstrap.js A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js R client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/list/list-view.js A client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js A client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M 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 A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js A client/galaxy/scripts/mvc/visualization/chart/chart-client.js A client/galaxy/scripts/mvc/visualization/chart/components/model.js A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js A client/galaxy/scripts/mvc/visualization/chart/views/description.js A client/galaxy/scripts/mvc/visualization/chart/views/editor.js A client/galaxy/scripts/mvc/visualization/chart/views/groups.js A client/galaxy/scripts/mvc/visualization/chart/views/menu.js A client/galaxy/scripts/mvc/visualization/chart/views/settings.js A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/async-save-text.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js R client/galaxy/style/less/autocomplete_tagging.less R client/galaxy/style/less/base.less R client/galaxy/style/less/bootstrap.less R client/galaxy/style/less/bootstrap/alerts.less R client/galaxy/style/less/bootstrap/badges.less R client/galaxy/style/less/bootstrap/bootstrap.less R client/galaxy/style/less/bootstrap/breadcrumbs.less R client/galaxy/style/less/bootstrap/button-groups.less R client/galaxy/style/less/bootstrap/buttons.less R client/galaxy/style/less/bootstrap/carousel.less R client/galaxy/style/less/bootstrap/close.less R client/galaxy/style/less/bootstrap/code.less R client/galaxy/style/less/bootstrap/component-animations.less R client/galaxy/style/less/bootstrap/dropdowns.less R client/galaxy/style/less/bootstrap/forms.less R client/galaxy/style/less/bootstrap/glyphicons.less R client/galaxy/style/less/bootstrap/grid.less R client/galaxy/style/less/bootstrap/input-groups.less R client/galaxy/style/less/bootstrap/jumbotron.less R client/galaxy/style/less/bootstrap/labels.less R client/galaxy/style/less/bootstrap/list-group.less R client/galaxy/style/less/bootstrap/media.less R client/galaxy/style/less/bootstrap/mixins.less R client/galaxy/style/less/bootstrap/modals.less R client/galaxy/style/less/bootstrap/navbar.less R client/galaxy/style/less/bootstrap/navs.less R client/galaxy/style/less/bootstrap/normalize.less R client/galaxy/style/less/bootstrap/pager.less R client/galaxy/style/less/bootstrap/pagination.less R client/galaxy/style/less/bootstrap/panels.less R client/galaxy/style/less/bootstrap/popovers.less R client/galaxy/style/less/bootstrap/print.less R client/galaxy/style/less/bootstrap/progress-bars.less R client/galaxy/style/less/bootstrap/responsive-utilities.less R client/galaxy/style/less/bootstrap/scaffolding.less R client/galaxy/style/less/bootstrap/tables.less R client/galaxy/style/less/bootstrap/theme.less R client/galaxy/style/less/bootstrap/thumbnails.less R client/galaxy/style/less/bootstrap/tooltip.less R client/galaxy/style/less/bootstrap/type.less R client/galaxy/style/less/bootstrap/utilities.less R client/galaxy/style/less/bootstrap/variables.less R client/galaxy/style/less/bootstrap/wells.less R client/galaxy/style/less/circster.less R client/galaxy/style/less/collection.less R client/galaxy/style/less/dataset.less R client/galaxy/style/less/embed_item.less R client/galaxy/style/less/flex.less R client/galaxy/style/less/fontawesome/bordered-pulled.less R client/galaxy/style/less/fontawesome/core.less R client/galaxy/style/less/fontawesome/fixed-width.less R client/galaxy/style/less/fontawesome/font-awesome.less R client/galaxy/style/less/fontawesome/icons.less R client/galaxy/style/less/fontawesome/larger.less R client/galaxy/style/less/fontawesome/list.less R client/galaxy/style/less/fontawesome/mixins.less R client/galaxy/style/less/fontawesome/path.less R client/galaxy/style/less/fontawesome/rotated-flipped.less R client/galaxy/style/less/fontawesome/spinning.less R client/galaxy/style/less/fontawesome/stacked.less R client/galaxy/style/less/fontawesome/variables.less R client/galaxy/style/less/frame.less R client/galaxy/style/less/galaxy_bootstrap.less R client/galaxy/style/less/galaxy_bootstrap/overrides.less R client/galaxy/style/less/galaxy_bootstrap/variables.less R client/galaxy/style/less/galaxy_variables.less R client/galaxy/style/less/history.less R client/galaxy/style/less/iconic_stroke.less R client/galaxy/style/less/job.less R client/galaxy/style/less/jstree.less R client/galaxy/style/less/library.less R client/galaxy/style/less/list-item.less R client/galaxy/style/less/reports.less R client/galaxy/style/less/select2.less R client/galaxy/style/less/theme/blue.less R client/galaxy/style/less/theme/plain.less R client/galaxy/style/less/toastr.less R client/galaxy/style/less/tour.less R client/galaxy/style/less/trackster.less R client/galaxy/style/less/ui.less R client/galaxy/style/less/ui/dataset-choice.less R client/galaxy/style/less/ui/error-modal.less R client/galaxy/style/less/ui/icon-btn.less R client/galaxy/style/less/ui/pagination.less R client/galaxy/style/less/ui/paired-collection-creator.less R client/galaxy/style/less/ui/peek-column-selector.less R client/galaxy/style/less/ui/search-input.less R client/galaxy/style/less/upload.less A client/galaxy/style/scss/autocomplete_tagging.scss A client/galaxy/style/scss/base.scss A client/galaxy/style/scss/charts.scss A client/galaxy/style/scss/circster.scss A client/galaxy/style/scss/collection.scss A client/galaxy/style/scss/dataset.scss A client/galaxy/style/scss/embed_item.scss A client/galaxy/style/scss/flex.scss A client/galaxy/style/scss/frame.scss A client/galaxy/style/scss/galaxy_bootstrap/overrides.scss A client/galaxy/style/scss/galaxy_bootstrap/variables.scss A client/galaxy/style/scss/galaxy_variables.scss A client/galaxy/style/scss/history.scss A client/galaxy/style/scss/iconic_stroke.scss A client/galaxy/style/scss/job.scss A client/galaxy/style/scss/jstree.scss A client/galaxy/style/scss/library.scss A client/galaxy/style/scss/list-item.scss A client/galaxy/style/scss/reports.scss A client/galaxy/style/scss/select2.scss A client/galaxy/style/scss/theme/blue.scss A client/galaxy/style/scss/theme/plain.scss A client/galaxy/style/scss/toastr.scss A client/galaxy/style/scss/tour.scss A client/galaxy/style/scss/trackster.scss A client/galaxy/style/scss/ui.scss A client/galaxy/style/scss/ui/dataset-choice.scss A client/galaxy/style/scss/ui/error-modal.scss A client/galaxy/style/scss/ui/icon-btn.scss A client/galaxy/style/scss/ui/pagination.scss A client/galaxy/style/scss/ui/paired-collection-creator.scss A client/galaxy/style/scss/ui/peek-column-selector.scss A client/galaxy/style/scss/ui/search-input.scss A client/galaxy/style/scss/upload.scss R client/grunt-tasks/style.js M client/gulpfile.js M client/karma.config.js M client/package.json A client/styleguide.config.js M client/webpack.config.js M client/yarn.lock M config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/job_conf.xml.sample_basic M config/job_metrics_conf.xml.sample M config/local_conda_mapping.yml.sample A config/oidc_backends_config.xml.sample A config/oidc_config.xml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/tours/core.scratchbook.yaml R config/plugins/visualizations/charts/config/charts.xml R config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/static/client/app.css R config/plugins/visualizations/charts/static/client/app.js R config/plugins/visualizations/charts/static/client/components/model.js R config/plugins/visualizations/charts/static/client/components/screenshot.js R config/plugins/visualizations/charts/static/client/views/description.js R config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/groups.js R config/plugins/visualizations/charts/static/client/views/settings.js R config/plugins/visualizations/charts/static/client/views/viewer.js R config/plugins/visualizations/charts/static/client/views/viewport.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map R config/plugins/visualizations/charts/static/repository/build/others_example.js R config/plugins/visualizations/charts/static/repository/build/others_example.js.map R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map R config/plugins/visualizations/charts/static/repository/build/registry.js R config/plugins/visualizations/charts/static/repository/build/registry.js.map R config/plugins/visualizations/charts/static/repository/build/registry.tmp.js R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js R config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js R config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js R config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js R config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js R config/plugins/visualizations/charts/static/repository/registry.json R config/plugins/visualizations/charts/static/repository/utilities/jobs.js R config/plugins/visualizations/charts/static/repository/utilities/sifjson.js R config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/templates/charts.mako R config/plugins/visualizations/charts/webpack.config.js A config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/csg/templates/csg.mako A config/plugins/visualizations/cytoscape/config/cytoscape.xml A config/plugins/visualizations/cytoscape/package.json A config/plugins/visualizations/cytoscape/src/script.js A config/plugins/visualizations/cytoscape/static/logo.png A config/plugins/visualizations/cytoscape/static/script.js A config/plugins/visualizations/drawrna/config/drawrna.xml A config/plugins/visualizations/drawrna/package.json A config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/naview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/radloop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/region.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/radiate/getradiate.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/link.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/linkcol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/ncanno.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residue.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residuecol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/structure.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/.Rhistory A config/plugins/visualizations/drawrna/src/drawrnajs/utils/lasso.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/parsedbr.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/spectrum.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/style.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/annoview.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/optspanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/seqpanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/vispanel.js A config/plugins/visualizations/drawrna/src/script.js A config/plugins/visualizations/drawrna/static/logo.png A config/plugins/visualizations/drawrna/static/script.js A config/plugins/visualizations/example/config/example.xml A config/plugins/visualizations/example/package.json A config/plugins/visualizations/example/src/script.js A config/plugins/visualizations/example/static/logo.png A config/plugins/visualizations/example/static/script.js M config/plugins/visualizations/graphviz/config/graphviz.xml R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js R config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js R config/plugins/visualizations/graphviz/static/js/tip_followscroll.js M config/plugins/visualizations/graphviz/templates/graphviz.mako A config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml A config/plugins/visualizations/heatmap/heatmap_cluster/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml A config/plugins/visualizations/heatmap/heatmap_default/package.json A config/plugins/visualizations/heatmap/heatmap_default/src/colorsets.js A config/plugins/visualizations/heatmap/heatmap_default/src/script.js A config/plugins/visualizations/heatmap/heatmap_default/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/static/script.js A config/plugins/visualizations/hivtrace/config/hivtrace.xml A config/plugins/visualizations/hivtrace/static/448c34a56d699c29117adc64c43affeb.woff2 A config/plugins/visualizations/hivtrace/static/674f50d287a8c48dc19ba404d20fe713.eot A config/plugins/visualizations/hivtrace/static/89889688147bd7575d6327160d64e760.svg A config/plugins/visualizations/hivtrace/static/912ec66d7572ff821749319396470bde.svg A config/plugins/visualizations/hivtrace/static/af7ae505a9eed503f8b8e6982036873e.woff2 A config/plugins/visualizations/hivtrace/static/b06871f281fee6b241d60582ae9369b9.ttf A config/plugins/visualizations/hivtrace/static/e18bbf611f2a2e43afc071aa2f4e1512.ttf A config/plugins/visualizations/hivtrace/static/f4769f9bdb7466be65088239c12046d1.eot A config/plugins/visualizations/hivtrace/static/fa2772327f55d8198301fdb8bcfc8158.woff A config/plugins/visualizations/hivtrace/static/fee66e712a8a08eef5805a46892932ad.woff A config/plugins/visualizations/hivtrace/static/hivtrace.css A config/plugins/visualizations/hivtrace/static/hivtrace.css.map A config/plugins/visualizations/hivtrace/static/hivtrace.js A config/plugins/visualizations/hivtrace/static/hivtrace.js.map A config/plugins/visualizations/hivtrace/static/logo.png A config/plugins/visualizations/hivtrace/static/vendor.js A config/plugins/visualizations/hivtrace/static/vendor.js.map A config/plugins/visualizations/hivtrace/templates/index.mako A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml A config/plugins/visualizations/jqplot/jqplot_bar/package.json A config/plugins/visualizations/jqplot/jqplot_bar/src/script.js A config/plugins/visualizations/jqplot/jqplot_bar/static/logo.png A config/plugins/visualizations/jqplot/jqplot_bar/static/script.css A config/plugins/visualizations/jqplot/jqplot_bar/static/script.js A config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml A config/plugins/visualizations/jqplot/jqplot_box/static/logo.png A config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml A config/plugins/visualizations/jqplot/jqplot_histogram/static/logo.png A config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml A config/plugins/visualizations/jqplot/jqplot_line/static/logo.png A config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml A config/plugins/visualizations/jqplot/jqplot_scatter/static/logo.png A config/plugins/visualizations/msa/config/msa.xml A config/plugins/visualizations/msa/package.json A config/plugins/visualizations/msa/src/msa.js A config/plugins/visualizations/msa/static/logo.png A config/plugins/visualizations/msa/static/script.js A config/plugins/visualizations/ngl/config/ngl.xml A config/plugins/visualizations/ngl/package.json A config/plugins/visualizations/ngl/src/ngl.js A config/plugins/visualizations/ngl/src/viewer.js A config/plugins/visualizations/ngl/static/logo.png A config/plugins/visualizations/ngl/static/ngl.js A config/plugins/visualizations/nvd3/nvd3_bar/.babelrc A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml A config/plugins/visualizations/nvd3/nvd3_bar/package.json A config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar/static/logo.png A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3/nvd3_bar_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml A config/plugins/visualizations/nvd3/nvd3_histogram/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml A config/plugins/visualizations/nvd3/nvd3_horizontal/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml A config/plugins/visualizations/nvd3/nvd3_line/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml A config/plugins/visualizations/nvd3/nvd3_line_focus/static/logo.png A config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml A config/plugins/visualizations/nvd3/nvd3_pie/static/logo.png A config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml A config/plugins/visualizations/nvd3/nvd3_scatter/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/static/logo.png A config/plugins/visualizations/phylocanvas/config/phylocanvas.xml A config/plugins/visualizations/phylocanvas/package.json A config/plugins/visualizations/phylocanvas/src/script.js A config/plugins/visualizations/phylocanvas/static/logo.png A config/plugins/visualizations/phylocanvas/static/script.js M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png A config/plugins/visualizations/pv/config/pv.xml A config/plugins/visualizations/pv/package.json A config/plugins/visualizations/pv/src/pv.js A config/plugins/visualizations/pv/static/logo.png A config/plugins/visualizations/pv/static/pv.js A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js A config/plugins/visualizations/scatterplot/src/numeric-column-stats.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/src/worker-stats.js A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js A config/plugins/visualizations/scatterplot/static/logo.png R config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js A config/plugins/visualizations/scatterplot/static/scatterplot.js R config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R config/plugins/visualizations/scatterplot/webpack.config.js M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/unipept/templates/unipept.mako A config/plugins/visualizations/venn/config/venn.xml A config/plugins/visualizations/venn/package.json A config/plugins/visualizations/venn/src/script.js A config/plugins/visualizations/venn/src/venn.js A config/plugins/visualizations/venn/static/logo.png A config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js M config/plugins/webhooks/demo/search/script.js M config/plugins/webhooks/demo/tour_generator/__init__.py M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample M config/tool_destinations.yml.sample M config/tool_shed.yml.sample M config/user_preferences_extra_conf.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M create_db.sh M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml A display_applications/intermine/intermine_simple.xml M doc/parse_gx_xsd.py M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/nginx.md M doc/source/admin/reports_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/performance_tracking.rst M doc/source/conf.py A doc/source/conf.versioning.py M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/project/organization.rst A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M extract_dataset_parts.sh M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py A lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py A lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml A lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_fai.xml M lib/galaxy/datatypes/converters/fasta_to_len.py R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.py A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml 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_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_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/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py R lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.fastqsanger.bz2 A lib/galaxy/datatypes/test/1.fastqsanger.gz A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.tiff A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/diamond.daa A lib/galaxy/datatypes/test/empty.txt M lib/galaxy/datatypes/test/example.iqtree A lib/galaxy/datatypes/test/test.blib M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/dynamic_tool_destination.py R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py A lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py A lib/galaxy/jobs/metrics/instrumenters/hostname.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.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/chronos.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py R lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py R lib/galaxy/jobs/runners/util/retry.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py A lib/galaxy/managers/cloud.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/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py A lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/apply_rules.xml M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py A lib/galaxy/tools/filter_empty_collection.xml M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/tools/repositories.py M lib/galaxy/tools/special_tools.py A lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py A lib/galaxy/util/create_history_template.py M lib/galaxy/util/facts.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/util/monitors.py M lib/galaxy/util/none_like.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/permutations.py A lib/galaxy/util/rules_dsl.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/script.py M lib/galaxy/util/validation.py A lib/galaxy/util/watcher.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/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/interactive_environments.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/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py A lib/galaxy/web/framework/helpers/tags.py M lib/galaxy/web/framework/middleware/batch.py R lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/web/framework/middleware/statsd.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/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/annotations.py A lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.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/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py A lib/galaxy/webapps/galaxy/api/uploads.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/config_schema.yml M lib/galaxy/webapps/galaxy/config_watchers.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py A lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/config_schema.yml M lib/galaxy/webapps/reports/controllers/query.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/config.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/controllers/admin.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/model/__init__.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/web_util.py M lib/tool_shed/util/workflow_util.py M manage_db.sh R openid/aol.xml M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/common.py A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py A scripts/docker_swarm_manager.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/maintenance.sh M scripts/manage_db.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/migrate_tools/migrate_tools.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh A scripts/plugin_staging.py M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A static/images/fonts/FontAwesome.otf M static/images/fonts/fontawesome-webfont.eot A static/images/fonts/fontawesome-webfont.svg M static/images/fonts/fontawesome-webfont.ttf M static/images/fonts/fontawesome-webfont.woff A static/images/fonts/fontawesome-webfont.woff2 R static/scripts/admin.toolshed.js R static/scripts/bundled/admin.bundled.js R static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/extended.bundled.js R static/scripts/bundled/libs.bundled.js R static/scripts/bundled/login.bundled.js R static/scripts/galaxy.interactive_environments.js R static/scripts/galaxy.js R static/scripts/galaxy.library.js R static/scripts/galaxy.pages.js R static/scripts/i18n.js R static/scripts/layout/generic-nav-view.js R static/scripts/layout/masthead.js R static/scripts/layout/menu.js R static/scripts/layout/modal.js R static/scripts/layout/page.js R static/scripts/layout/panel.js R static/scripts/layout/router.js R static/scripts/layout/scratchbook.js R static/scripts/legacy/grid/grid-model.js R static/scripts/legacy/grid/grid-template.js R static/scripts/legacy/grid/grid-view.js R static/scripts/libs/backbone.js R static/scripts/libs/bbi/bigwig.js R static/scripts/libs/bbi/jquery-ajax-native.js R static/scripts/libs/bbi/jszlib.js R static/scripts/libs/bbi/spans.js R static/scripts/libs/bibtexParse.js R static/scripts/libs/bootstrap-tour.js R static/scripts/libs/bootstrap.js R static/scripts/libs/d3.js R static/scripts/libs/farbtastic.js R static/scripts/libs/jquery.sparklines.js R static/scripts/libs/jquery/jquery-ui.js R static/scripts/libs/jquery/jquery.autocomplete.js R static/scripts/libs/jquery/jquery.complexify.js R static/scripts/libs/jquery/jquery.cookie.js R static/scripts/libs/jquery/jquery.dynatree.js R static/scripts/libs/jquery/jquery.event.drag.js R static/scripts/libs/jquery/jquery.event.drop.js R static/scripts/libs/jquery/jquery.event.hover.js R static/scripts/libs/jquery/jquery.form.js R static/scripts/libs/jquery/jquery.js R static/scripts/libs/jquery/jquery.migrate.js R static/scripts/libs/jquery/jquery.mousewheel.js R static/scripts/libs/jquery/jquery.rating.js R static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/jquery/jstorage.js R static/scripts/libs/jquery/jstree.js R static/scripts/libs/jquery/select2.js R static/scripts/libs/raven.js R static/scripts/libs/require.js R static/scripts/libs/toastr.js R static/scripts/libs/underscore.js R static/scripts/mvc/annotation.js R static/scripts/mvc/base-mvc.js R static/scripts/mvc/base/controlled-fetch-collection.js R static/scripts/mvc/collection/base-creator.js R static/scripts/mvc/collection/collection-li-edit.js R static/scripts/mvc/collection/collection-li.js R static/scripts/mvc/collection/collection-model.js R static/scripts/mvc/collection/collection-view-edit.js R static/scripts/mvc/collection/collection-view.js R static/scripts/mvc/collection/list-collection-creator.js R static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/collection/pair-collection-creator.js R static/scripts/mvc/dataset/data.js R static/scripts/mvc/dataset/dataset-choice.js R static/scripts/mvc/dataset/dataset-edit-attributes.js R static/scripts/mvc/dataset/dataset-error.js R static/scripts/mvc/dataset/dataset-li-edit.js R static/scripts/mvc/dataset/dataset-li.js R static/scripts/mvc/dataset/dataset-list.js R static/scripts/mvc/dataset/dataset-model.js R static/scripts/mvc/dataset/states.js R static/scripts/mvc/form/form-data.js R static/scripts/mvc/form/form-input.js R static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-repeat.js R static/scripts/mvc/form/form-section.js R static/scripts/mvc/form/form-view.js R static/scripts/mvc/form/form-wrapper.js R static/scripts/mvc/grid/grid-model.js R static/scripts/mvc/grid/grid-shared.js R static/scripts/mvc/grid/grid-template.js R static/scripts/mvc/grid/grid-view.js R static/scripts/mvc/history/copy-dialog.js R static/scripts/mvc/history/hda-li-edit.js R static/scripts/mvc/history/hda-li.js R static/scripts/mvc/history/hda-model.js R static/scripts/mvc/history/hdca-li-edit.js R static/scripts/mvc/history/hdca-li.js R static/scripts/mvc/history/hdca-model.js R static/scripts/mvc/history/history-content-model.js R static/scripts/mvc/history/history-contents.js R static/scripts/mvc/history/history-item-li.js R static/scripts/mvc/history/history-list.js R static/scripts/mvc/history/history-model.js R static/scripts/mvc/history/history-preferences.js R static/scripts/mvc/history/history-structure-view.js R static/scripts/mvc/history/history-view-annotated.js R static/scripts/mvc/history/history-view-edit-current.js R static/scripts/mvc/history/history-view-edit.js R static/scripts/mvc/history/history-view.js R static/scripts/mvc/history/job-dag.js R static/scripts/mvc/history/job-states-model.js R static/scripts/mvc/history/multi-panel.js R static/scripts/mvc/history/options-menu.js R static/scripts/mvc/job/job-li.js R static/scripts/mvc/job/job-model.js R static/scripts/mvc/job/job-params.js R static/scripts/mvc/lazy/lazy-limited.js R static/scripts/mvc/library/library-dataset-view.js R static/scripts/mvc/library/library-folder-view.js R static/scripts/mvc/library/library-folderlist-view.js R static/scripts/mvc/library/library-folderrow-view.js R static/scripts/mvc/library/library-foldertoolbar-view.js R static/scripts/mvc/library/library-library-view.js R static/scripts/mvc/library/library-librarylist-view.js R static/scripts/mvc/library/library-libraryrow-view.js R static/scripts/mvc/library/library-librarytoolbar-view.js R static/scripts/mvc/library/library-model.js R static/scripts/mvc/library/library-util.js R static/scripts/mvc/list/list-item.js R static/scripts/mvc/list/list-view.js R static/scripts/mvc/tag.js R static/scripts/mvc/tool/tool-form-base.js R static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form.js R static/scripts/mvc/tool/tool-genomespace.js R static/scripts/mvc/tool/tools.js R static/scripts/mvc/toolshed/categories-view.js R static/scripts/mvc/toolshed/repo-queue-view.js R static/scripts/mvc/toolshed/repo-status-view.js R static/scripts/mvc/toolshed/repositories-view.js R static/scripts/mvc/toolshed/repository-queue-view.js R static/scripts/mvc/toolshed/repository-view.js R static/scripts/mvc/toolshed/shed-list-view.js R static/scripts/mvc/toolshed/toolshed-model.js R static/scripts/mvc/toolshed/util.js R static/scripts/mvc/toolshed/workflows-view.js R static/scripts/mvc/tours.js R static/scripts/mvc/ui/error-modal.js R static/scripts/mvc/ui/icon-button.js R static/scripts/mvc/ui/popup-menu.js R static/scripts/mvc/ui/ui-buttons.js R static/scripts/mvc/ui/ui-color-picker.js R static/scripts/mvc/ui/ui-drilldown.js R static/scripts/mvc/ui/ui-frames.js R static/scripts/mvc/ui/ui-list.js R static/scripts/mvc/ui/ui-misc.js R static/scripts/mvc/ui/ui-modal.js R static/scripts/mvc/ui/ui-options.js R static/scripts/mvc/ui/ui-popover.js R static/scripts/mvc/ui/ui-portlet.js R static/scripts/mvc/ui/ui-select-content.js R static/scripts/mvc/ui/ui-select-default.js R static/scripts/mvc/ui/ui-select-ftp.js R static/scripts/mvc/ui/ui-select-genomespace.js R static/scripts/mvc/ui/ui-select-library.js R static/scripts/mvc/ui/ui-select.js R static/scripts/mvc/ui/ui-slider.js R static/scripts/mvc/ui/ui-table.js R static/scripts/mvc/ui/ui-tabs.js R static/scripts/mvc/ui/ui-thumbnails.js R static/scripts/mvc/upload/collection/collection-row.js R static/scripts/mvc/upload/collection/collection-view.js R static/scripts/mvc/upload/composite/composite-row.js R static/scripts/mvc/upload/composite/composite-view.js R static/scripts/mvc/upload/default/default-row.js R static/scripts/mvc/upload/default/default-view.js R static/scripts/mvc/upload/upload-button.js R static/scripts/mvc/upload/upload-extension.js R static/scripts/mvc/upload/upload-ftp.js R static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-settings.js R static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/user-custom-builds.js R static/scripts/mvc/user/user-model.js R static/scripts/mvc/user/user-preferences.js R static/scripts/mvc/user/user-quotameter.js R static/scripts/mvc/visualization/visualization-model.js R static/scripts/mvc/webhooks.js R static/scripts/mvc/workflow/workflow-canvas.js R static/scripts/mvc/workflow/workflow-connector.js R static/scripts/mvc/workflow/workflow-forms.js R static/scripts/mvc/workflow/workflow-icons.js R static/scripts/mvc/workflow/workflow-manager.js R static/scripts/mvc/workflow/workflow-model.js R static/scripts/mvc/workflow/workflow-node.js R static/scripts/mvc/workflow/workflow-terminals.js R static/scripts/mvc/workflow/workflow-view-data.js R static/scripts/mvc/workflow/workflow-view-node.js R static/scripts/mvc/workflow/workflow-view-terminals.js R static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js R static/scripts/nls/de/locale.js R static/scripts/nls/es/locale.js R static/scripts/nls/fr/locale.js R static/scripts/nls/ja/locale.js R static/scripts/nls/locale.js R static/scripts/nls/zh/locale.js R static/scripts/onload.js R static/scripts/packed R static/scripts/polyfills.js R static/scripts/reports/run_stats.js R static/scripts/toolshed/groups/group-detail-view.js R static/scripts/toolshed/groups/group-list-view.js R static/scripts/toolshed/groups/group-listrow-view.js R static/scripts/toolshed/groups/group-model.js R static/scripts/toolshed/toolshed.groups.js R static/scripts/ui/autocom_tagging.js R static/scripts/ui/editable-text.js R static/scripts/ui/fa-icon-button.js R static/scripts/ui/filter-control.js R static/scripts/ui/hoverhighlight.js R static/scripts/ui/loading-indicator.js R static/scripts/ui/mode-button.js R static/scripts/ui/pagination.js R static/scripts/ui/peek-column-selector.js R static/scripts/ui/popupmenu.js R static/scripts/ui/scroll-panel.js R static/scripts/ui/search-input.js R static/scripts/utils/add-logging.js R static/scripts/utils/ajax-queue.js R static/scripts/utils/async-save-text.js R static/scripts/utils/config.js R static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.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/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample R templates/admin/impersonate.mako R templates/admin/view_data_tables_registry.mako R templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/display_common.mako M templates/ind_share_base.mako M templates/js-app.mako R templates/sharing_base.mako M templates/show_params.mako M templates/tagging_common.mako M templates/user/login.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/structure.mako R templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako A test-data/1.csv A test-data/1.tiff A test-data/11.tabular A test-data/configfile.json A test-data/example-bag.zip A test-data/filter1_in6.bed A test-data/filter1_test6.bed A test-data/new_tags_1.txt A test-data/qname_sorted.bam A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt A test-data/sort_out1.bed A test-data/sort_out2.bed A test-data/sort_out3.tab A test-data/sort_out4.sam A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_visualizations.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/api.py A test/base/data/rules_dsl_spec.yml M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/populators.py A test/base/rules_test_data.py M test/base/testcase.py R test/base/tool_shed_util.py A test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml A test/functional/tools/collection_type_source_map_over.xml A test/functional/tools/column_param_configfile.xml A test/functional/tools/empty_select.xml A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/for_workflows/cat_collection.xml A test/functional/tools/identifier_single_in_repeat.xml A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/job_properties.xml M test/functional/tools/multi_data_optional.xml M test/functional/tools/multi_output_recurse.xml A test/functional/tools/output_action_change_format_paired.xml R test/functional/tools/paired_collection_map_over_structured_like.xml R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_data_manager_table_reload.py A test/integration/test_scripts.py A test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py A test/unit/datatypes/test_datatypes_registry.py A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_params.py M test/unit/managers/test_HistoryManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_remote_shell.py A test/unit/test_rule_utils.py M test/unit/test_security_helper.py A test/unit/test_security_passwords.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_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_validation.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/cutWrapper.pl M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into select_tag_parameter Commit: d417e9b239309707274011d4199b8f827fcc0f6d https://github.com/galaxyproject/galaxy/commit/d417e9b239309707274011d4199b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Flush out collection tag parameters a bit. - Switch select_tag to group_tag as a parameter name - since it is restricted to group_tags and we don't call data parameters select_data. - Add minimal XSD documentation for this new parameter type. - Add example tools - for single and multiple tags. - Add API tests for these tools and the tag handling. Commit: e5c532298d5db34da04d8f046ebe44abddbbaa64 https://github.com/galaxyproject/galaxy/commit/e5c532298d5db34da04d8f046ebe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Make tag order stable when using group_tag parameters. Commit: 6677e7b91385d027989613bdc621108da76e8425 https://github.com/galaxyproject/galaxy/commit/6677e7b91385d027989613bdc621… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix failing import/export test for group_tag changes. Commit: 5a914b9fa71ff2c00d7ba1a7c1dc3ccbb8437eae https://github.com/galaxyproject/galaxy/commit/5a914b9fa71ff2c00d7ba1a7c1dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Keep all user-selected tags, including duplicates Commit: 95e8a3491280cc26d435bebc1cf03488d7db3b88 https://github.com/galaxyproject/galaxy/commit/95e8a3491280cc26d435bebc1cf0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Correct copy-pasted docstring Commit: 55436c38008c3d1b261b7d9dfc728cc968bd6622 https://github.com/galaxyproject/galaxy/commit/55436c38008c3d1b261b7d9dfc72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml M test/functional/tools/samples_tool_conf.xml M test/unit/test_objectstore.py M test/unit/tools/test_wrappers.py Log Message: ----------- Merge pull request #5457 from mvdbeek/select_tag_parameter Allow selecting subset of collection by group tag Compare: https://github.com/galaxyproject/galaxy/compare/d1423b6e18cb...55436c38008c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0