April 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 773539: Move scripts out of lib/tool_shed.
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77353902ee7f7c06b6376537809b9b3ea700c84a https://github.com/galaxyproject/galaxy/commit/77353902ee7f7c06b6376537809b… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: R lib/tool_shed/scripts/api/add_repository_registry_entry.py R lib/tool_shed/scripts/api/common.py R lib/tool_shed/scripts/api/create_categories.py R lib/tool_shed/scripts/api/create_users.py R lib/tool_shed/scripts/api/export.py R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py R lib/tool_shed/scripts/api/import_capsule.py R lib/tool_shed/scripts/api/remove_repository_registry_entry.py R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_repositories_for_functional_tests.py R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py A scripts/tool_shed/api/add_repository_registry_entry.py A scripts/tool_shed/api/common.py A scripts/tool_shed/api/create_categories.py A scripts/tool_shed/api/create_users.py A scripts/tool_shed/api/export.py A scripts/tool_shed/api/get_filtered_repository_revisions.py A scripts/tool_shed/api/import_capsule.py A scripts/tool_shed/api/remove_repository_registry_entry.py A scripts/tool_shed/api/reset_metadata_on_repositories.py A scripts/tool_shed/api/tool_shed_repository_revision_update.py A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_repositories_for_functional_tests.py A scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_tool_dependency_definition_repositories.py A scripts/tool_shed/clean_up_tool_dependency_directory.py A scripts/tool_shed/deprecate_repositories_without_metadata.py A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Move scripts out of lib/tool_shed. Commit: 9bf3976e8a267d3f3d462c9d8f2798f9834024bb https://github.com/galaxyproject/galaxy/commit/9bf3976e8a267d3f3d462c9d8f27… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M scripts/tool_shed/api/common.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py Log Message: ----------- Fix sys.path.insert Commit: 9f1490cc60d993f9ac3907bdf53c0a65e7cbeadf https://github.com/galaxyproject/galaxy/commit/9f1490cc60d993f9ac3907bdf53c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Fix sys.path.insert some more. Commit: fbf8cfce2a89dd1c199bb757a55dfabeca9f9b7e https://github.com/galaxyproject/galaxy/commit/fbf8cfce2a89dd1c199bb757a55d… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M scripts/tool_shed/api/get_filtered_repository_revisions.py Log Message: ----------- Remove unused import. Commit: 2744d5541f7c1722d56eef7ea22c061cea6e2625 https://github.com/galaxyproject/galaxy/commit/2744d5541f7c1722d56eef7ea22c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: R lib/tool_shed/scripts/api/add_repository_registry_entry.py R lib/tool_shed/scripts/api/common.py R lib/tool_shed/scripts/api/create_categories.py R lib/tool_shed/scripts/api/create_users.py R lib/tool_shed/scripts/api/export.py R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py R lib/tool_shed/scripts/api/import_capsule.py R lib/tool_shed/scripts/api/remove_repository_registry_entry.py R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_repositories_for_functional_tests.py R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py A scripts/tool_shed/api/add_repository_registry_entry.py A scripts/tool_shed/api/common.py A scripts/tool_shed/api/create_categories.py A scripts/tool_shed/api/create_users.py A scripts/tool_shed/api/export.py A scripts/tool_shed/api/get_filtered_repository_revisions.py A scripts/tool_shed/api/import_capsule.py A scripts/tool_shed/api/remove_repository_registry_entry.py A scripts/tool_shed/api/reset_metadata_on_repositories.py A scripts/tool_shed/api/tool_shed_repository_revision_update.py A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_repositories_for_functional_tests.py A scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_tool_dependency_definition_repositories.py A scripts/tool_shed/clean_up_tool_dependency_directory.py A scripts/tool_shed/deprecate_repositories_without_metadata.py A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py Log Message: ----------- Merge pull request #2093 from davebx/move_scripts Move scripts out of lib/tool_shed. Compare: https://github.com/galaxyproject/galaxy/compare/ef604a75e518...2744d5541f7c

1 0

[galaxyproject/galaxy] febade: Convert the DRMAA runner to use Pulsar's DRMAA ses...
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: febadeae65cb61f52a497f2ddc2e3c9ec64e6ce3 https://github.com/galaxyproject/galaxy/commit/febadeae65cb61f52a497f2ddc2e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Convert the DRMAA runner to use Pulsar's DRMAA session wrapper Commit: a6af938ea424590fda3f0d0091dfb1ceb79f65f4 https://github.com/galaxyproject/galaxy/commit/a6af938ea424590fda3f0d0091df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix linting errors Commit: edd23f7c7a31e1d5113fbe82ae09324c67faf2d0 https://github.com/galaxyproject/galaxy/commit/edd23f7c7a31e1d5113fbe82ae09… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Bump pulsar-galaxy-lib version Commit: ef604a75e51800de5cc360f8bee1203b68b86a07 https://github.com/galaxyproject/galaxy/commit/ef604a75e51800de5cc360f8bee1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #2102 from natefoo/global-drmaa-session Convert the DRMAA runner to use Pulsar's DRMAA session wrapper Compare: https://github.com/galaxyproject/galaxy/compare/87ff0e38fa95...ef604a75e518

1 0

[galaxyproject/galaxy] 543a99: Fix data type list in editor
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 543a999dfa9e60eac02f7be5e9938ea9d1bad956 https://github.com/galaxyproject/galaxy/commit/543a999dfa9e60eac02f7be5e993… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Fix data type list in editor Commit: 87ff0e38fa95ef911b22f31a7adc3bff87cdef54 https://github.com/galaxyproject/galaxy/commit/87ff0e38fa95ef911b22f31a7adc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Merge pull request #2105 from guerler/fix_data_type_000 Fix datatype list in workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/40953369e69c...87ff0e38fa95

1 0

[galaxyproject/galaxy] ab242a: fixed bug with cli runner analogous to https://git...
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab242a84b11b2e5355e5e4b01d15f3528ad0a681 https://github.com/galaxyproject/galaxy/commit/ab242a84b11b2e5355e5e4b01d15… Author: Thomas Wollmann <thomas.wollmann(a)bioquant.uni-heidelberg.de> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- fixed bug with cli runner analogous to https://github.com/dpryan79/galaxy/commit/3536ff923cf736b2dbefab3e04b7fcd79… Commit: 987aac34bb42e8837b9d80992a44cdf9b85e24b3 https://github.com/galaxyproject/galaxy/commit/987aac34bb42e8837b9d80992a44… Author: Thomas Wollmann <thomas.wollmann(a)bioquant.uni-heidelberg.de> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- removed comment Commit: 91c4ccfc907b3199b2cea43816ac93cb083ebda6 https://github.com/galaxyproject/galaxy/commit/91c4ccfc907b3199b2cea43816ac… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- added default DEFAULT_EMBED_METADATA_IN_JOB value Commit: 4e15dc4e74c28eb0adfb57c8c863f4e1017a5790 https://github.com/galaxyproject/galaxy/commit/4e15dc4e74c28eb0adfb57c8c863… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- typo Commit: 0548e8ed306d4b00e0fd991e38a582f9723da1b3 https://github.com/galaxyproject/galaxy/commit/0548e8ed306d4b00e0fd991e38a5… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- added missing import Commit: bf8292ecc1d547e344e032ec92090ad7fee8f8a1 https://github.com/galaxyproject/galaxy/commit/bf8292ecc1d547e344e032ec9209… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- fixed lint error Commit: fb26d27b97e968969d3f5222df4daa764efb24ac https://github.com/galaxyproject/galaxy/commit/fb26d27b97e968969d3f5222df4d… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- fixed lint error Commit: 40953369e69cc8a4467a6c8560a93227c52dba2d https://github.com/galaxyproject/galaxy/commit/40953369e69cc8a4467a6c8560a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Merge pull request #2107 from ThomasWollmann/master Fix cli runner: use embed_metadata_in_job parameter Compare: https://github.com/galaxyproject/galaxy/compare/a85d6d556655...40953369e69c

1 0

[galaxyproject/galaxy] 9ecf99: make dependencies browsable again
by GitHub 07 Apr '16

07 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 9ecf99c227466a586a6299e37555655f5ff79a25 https://github.com/galaxyproject/galaxy/commit/9ecf99c227466a586a6299e37555… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- make dependencies browsable again it would be denied previously as the dependency folder is outside of the repository (symlink protection) Commit: 0882b4d8fb31752f1fa8c963c3f260f975c918f7 https://github.com/galaxyproject/galaxy/commit/0882b4d8fb31752f1fa8c963c3f2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- use proper method for detecting admin Commit: 50268cb8ca4a5f812346a71cc640141781f22a3d https://github.com/galaxyproject/galaxy/commit/50268cb8ca4a5f812346a71cc640… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- fix missing call; add docs and refactor a bit Commit: 455113d182236a0fec880db296b746a413a8edc4 https://github.com/galaxyproject/galaxy/commit/455113d182236a0fec880db296b7… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #2101 from martenson/fix-browsing-dependencies [16.01] make dependencies browsable again Compare: https://github.com/galaxyproject/galaxy/compare/040410b1d3f0...455113d18223

1 0

[galaxyproject/infrastructure-playbook] 1fbaed: Reinstalled the slurm controller and CVMFS stratum...
by GitHub 07 Apr '16

07 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1fbaed1102efe4171d77077175edcb0249ec80ac https://github.com/galaxyproject/infrastructure-playbook/commit/1fbaed1102e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M ansible.cfg M galaxyenv/group_vars/cvmfsstratum1servers.yml A galaxyenv/host_vars/cvmfs1-iu0.galaxyproject.org.yml M galaxyenv/playbook.yml M jetstreamiuenv/group_vars/cvmfsclients.yml M jetstreamiuenv/group_vars/slurmclients.yml R jetstreamiuenv/group_vars/slurmservers.yml M jetstreamiuenv/inventory M jetstreamiuenv/playbook.yml M jetstreamiuenv/templates/slurm/slurm.conf.j2 M roles/slurm/tasks/main.yml Log Message: ----------- Reinstalled the slurm controller and CVMFS stratum1 at TACC w/ static fixed IP

1 0

[galaxyproject/galaxy] c9db3f: Alternative stricter csv formats
by GitHub 07 Apr '16

07 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9db3f56bbe70ea3d578d16985c5c38c73ec5e42 https://github.com/galaxyproject/galaxy/commit/c9db3f56bbe70ea3d578d16985c5… Author: Christian-B <github(a)brenn.co.uk> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Alternative stricter csv formats Commit: fa7ccdf4b07598f5ebdfb1400f0bec2e2dabc164 https://github.com/galaxyproject/galaxy/commit/fa7ccdf4b07598f5ebdfb1400f0b… Author: Christian-B <github(a)brenn.co.uk> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Flake8 fix Commit: 79a7e31da7e6151c64b32f911fc60fcbdb78bba2 https://github.com/galaxyproject/galaxy/commit/79a7e31da7e6151c64b32f911fc6… Author: Christian-B <github(a)brenn.co.uk> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Remove bug log statement Commit: 7a960b08521ffa00e2984434aa870a49a96da0b5 https://github.com/galaxyproject/galaxy/commit/7a960b08521ffa00e2984434aa87… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-04 (Mon, 04 Jan 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py Log Message: ----------- Small tweaks to CSV fixes by @Christian-B. - Update sample datatype conf. - Use Python naming conventions and PEP-8 style fixes. Commit: 132ff18db68db6bd611dd94ed988d4c5f6d1dee5 https://github.com/galaxyproject/galaxy/commit/132ff18db68db6bd611dd94ed988… Author: Christian Y. Brenninkmeijer <christian.brenninkmeijer(a)manchester.ac.uk> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #1 from jmchilton/csv_fix Small tweaks to CSV fixes by @Christian-B. Commit: de506dec0c52e655a3fdff96368a288b6c454cde https://github.com/galaxyproject/galaxy/commit/de506dec0c52e655a3fdff96368a… Author: Christian-B <github(a)brenn.co.uk> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- fixed spelling found by @nsoranzo Commit: 7e0427b8b7d0f3de78175d254baff058bb0fce28 https://github.com/galaxyproject/galaxy/commit/7e0427b8b7d0f3de78175d254baf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh A .ci/first_startup.sh M .ci/flake8_blacklist.txt A .ci/flake8_py3_wrapper.sh A .ci/py3_sources.txt M .gitignore M .travis.yml A Makefile M README.rst A client/.docker-build.sh A client/Dockerfile M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/layout/page.js A client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/IE/IE7.js R client/galaxy/scripts/libs/IE/IE8.js R client/galaxy/scripts/libs/IE/blank.gif R client/galaxy/scripts/libs/IE/excanvas.js R client/galaxy/scripts/libs/IE/ie7-recalc.js A client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/backbone/backbone.js A client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js R client/galaxy/scripts/libs/handlebars.runtime.js A client/galaxy/scripts/mvc/annotation.js R client/galaxy/scripts/mvc/annotations.js R client/galaxy/scripts/mvc/app/app-analysis.js R client/galaxy/scripts/mvc/app/app-login.js R client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js R client/galaxy/scripts/mvc/collection/collection-panel-edit.js R client/galaxy/scripts/mvc/collection/collection-panel.js A client/galaxy/scripts/mvc/collection/collection-view-edit.js A client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-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 R client/galaxy/scripts/mvc/data.js A client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js R client/galaxy/scripts/mvc/history/history-panel-annotated.js R client/galaxy/scripts/mvc/history/history-panel-edit-current.js R client/galaxy/scripts/mvc/history/history-panel-edit.js R client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/history-structure-view.js A client/galaxy/scripts/mvc/history/history-view-annotated.js A client/galaxy/scripts/mvc/history/history-view-edit-current.js A client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/list/list-item.js R client/galaxy/scripts/mvc/list/list-panel.js A client/galaxy/scripts/mvc/list/list-view.js A client/galaxy/scripts/mvc/tag.js R client/galaxy/scripts/mvc/tags.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js A client/galaxy/scripts/mvc/tool/tools.js R client/galaxy/scripts/mvc/tools.js R client/galaxy/scripts/mvc/tools/tools-form-base.js R client/galaxy/scripts/mvc/tools/tools-form-workflow.js R client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/tools/tools-jobs.js R client/galaxy/scripts/mvc/tools/tools-template.js A client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/popup-menu.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-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-ftp.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.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 M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-connector.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.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js A client/galaxy/scripts/onload.js A client/galaxy/scripts/polyfills.js R client/galaxy/scripts/rgenetics/checkbox_and_radiobutton.js R client/galaxy/scripts/rgenetics/helper_functions.js R client/galaxy/scripts/rgenetics/timer.js R client/galaxy/scripts/templates/compiled/panel_section.js R client/galaxy/scripts/templates/compiled/tool_form.js R client/galaxy/scripts/templates/compiled/tool_link.js R client/galaxy/scripts/templates/compiled/tool_search.js R client/galaxy/scripts/templates/panel_section.handlebars R client/galaxy/scripts/templates/tool_form.handlebars R client/galaxy/scripts/templates/tool_link.handlebars R client/galaxy/scripts/templates/tool_search.handlebars R client/galaxy/scripts/tools/rgenetics/checkbox_and_radiobutton.js R client/galaxy/scripts/tools/rgenetics/helper_functions.js R client/galaxy/scripts/tools/rgenetics/timer.js A client/galaxy/scripts/ui/autocom_tagging.js A client/galaxy/scripts/ui/editable-text.js A client/galaxy/scripts/ui/popupmenu.js A client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/ajax-queue.js A client/galaxy/scripts/utils/async-save-text.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/trackster/util.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/frame.less M client/galaxy/style/less/library.less R client/galaxy/style/less/masthead.less A client/galaxy/style/less/tour.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/icon-btn.less M client/galaxy/style/less/upload.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js R client/grunt-tasks/templates.js A client/grunt-tasks/webpack.js M client/package.json A client/webpack.config.js M config/datatypes_conf.xml.sample A config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/common/templates/ie.mako R config/plugins/interactive_environments/ipython/config/ipython.ini.sample R config/plugins/interactive_environments/ipython/config/ipython.xml R config/plugins/interactive_environments/ipython/static/js/ipython.js R config/plugins/interactive_environments/ipython/templates/ipython.mako R config/plugins/interactive_environments/ipython/templates/notebook.ipynb A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako A config/plugins/tours/core.galaxy_ui.yaml A config/plugins/tours/core.history.yaml A config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/charts/Gruntfile.js R config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/templates/charts.mako A config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/Detector.js A config/plugins/visualizations/csg/static/OrbitControls.js A config/plugins/visualizations/csg/static/PLYLoader.js A config/plugins/visualizations/csg/static/VTKLoader.js A config/plugins/visualizations/csg/static/dat.gui.min.js A config/plugins/visualizations/csg/static/three.min.js A config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/scatterplot/Gruntfile.js M config/plugins/visualizations/scatterplot/package.json R config/plugins/visualizations/scatterplot/src/handlebars/chartcontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/editor.handlebars M config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A config/reports.ini.sample R config/reports_wsgi.ini.sample M config/tool_conf.xml.sample M config/tool_shed.ini.sample A doc/source/admin/dependency_resolvers.rst A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/dev/faq.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/project/issues.rst M doc/source/project/organization.rst A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01.rst A doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/constructive_solid_geometry.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.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/test.idpDB A lib/galaxy/datatypes/test/test.mz5 M lib/galaxy/datatypes/text.py A lib/galaxy/datatypes/triples.py A lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/ratable.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/visualizations.py M lib/galaxy/managers/workflows.py R lib/galaxy/metadata M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.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 A lib/galaxy/tools/deps/views.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.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/meta.py R lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py A lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py A lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_collection_def.py A lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/special_tools.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/wrappers.py A lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py A lib/galaxy/util/checkers.py R lib/galaxy/util/debugging.py A lib/galaxy/util/dictifiable.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/directory_hash.py M lib/galaxy/util/expressions.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py R lib/galaxy/util/lrucache.py A lib/galaxy/util/multi_byte.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/properties.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/topsort.py A lib/galaxy/util/ucsc.py M lib/galaxy/util/validation.py M lib/galaxy/util/xml_macros.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/remote_files.py A lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py A lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/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/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/tool_shed/capsule/capsule_manager.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/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M requirements.txt M run.sh M run_reports.sh M run_tests.sh M scripts/api/common.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/create.py M scripts/api/data_manager_example_execute.py M scripts/api/delete.py M scripts/api/display.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/binary_compatibility.py M scripts/bootstrap_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/edam_mapping.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py A scripts/patch.sh M scripts/set_dataset_sizes.py R scripts/set_metadata.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py R set_metadata.sh A static/incompatible-browser.html R static/maps/base.js.map R static/maps/galaxy.autocom_tagging.js.map R static/maps/galaxy.base.js.map R static/maps/galaxy.frame.js.map A static/maps/galaxy.js.map M static/maps/galaxy.library.js.map R static/maps/galaxy.masthead.js.map M static/maps/galaxy.menu.js.map M static/maps/galaxy.pages.js.map R static/maps/galaxy.panels.js.map R static/maps/galaxy.tools.js.map R static/maps/galaxy.ui.scrollPanel.js.map R static/maps/galaxy.workflows.js.map A static/maps/layout/masthead.js.map A static/maps/layout/menu.js.map A static/maps/layout/modal.js.map A static/maps/layout/page.js.map A static/maps/layout/panel.js.map A static/maps/layout/scratchbook.js.map R static/maps/libs/IE/IE7.js.map R static/maps/libs/IE/IE8.js.map R static/maps/libs/IE/excanvas.js.map R static/maps/libs/IE/ie7-recalc.js.map A static/maps/libs/backbone.js.map R static/maps/libs/backbone/backbone.js.map A static/maps/libs/bootstrap-tour.js.map A static/maps/libs/common-libs.js.map R static/maps/libs/handlebars.runtime.js.map A static/maps/mvc/annotation.js.map R static/maps/mvc/annotations.js.map R static/maps/mvc/app/app-analysis.js.map R static/maps/mvc/app/app-login.js.map R static/maps/mvc/app/app-view.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map R static/maps/mvc/collection/collection-panel-edit.js.map R static/maps/mvc/collection/collection-panel.js.map A static/maps/mvc/collection/collection-view-edit.js.map A static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map R static/maps/mvc/data.js.map A static/maps/mvc/dataset/data.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/dataset/states.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map R static/maps/mvc/history/history-panel-annotated.js.map R static/maps/mvc/history/history-panel-edit-current.js.map R static/maps/mvc/history/history-panel-edit.js.map R static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/history-structure-view.js.map A static/maps/mvc/history/history-view-annotated.js.map A static/maps/mvc/history/history-view-edit-current.js.map A static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/job-dag.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/list/list-item.js.map A static/maps/mvc/list/list-view.js.map A static/maps/mvc/tag.js.map R static/maps/mvc/tags.js.map A static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-template.js.map A static/maps/mvc/tool/tools.js.map R static/maps/mvc/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map R static/maps/mvc/tools/tools-form-workflow.js.map R static/maps/mvc/tools/tools-form.js.map R static/maps/mvc/tools/tools-jobs.js.map R static/maps/mvc/tools/tools-template.js.map A static/maps/mvc/tours.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map A static/maps/onload.js.map A static/maps/polyfills.js.map R static/maps/rgenetics/checkbox_and_radiobutton.js.map R static/maps/rgenetics/helper_functions.js.map R static/maps/rgenetics/timer.js.map M static/maps/templates/compiled/panel_section.js.map M static/maps/templates/compiled/tool_form.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/templates/compiled/tool_search.js.map R static/maps/tools/rgenetics/checkbox_and_radiobutton.js.map R static/maps/tools/rgenetics/helper_functions.js.map R static/maps/tools/rgenetics/timer.js.map A static/maps/ui/autocom_tagging.js.map A static/maps/ui/editable-text.js.map A static/maps/ui/popupmenu.js.map A static/maps/ui/scroll-panel.js.map M static/maps/utils/ajax-queue.js.map A static/maps/utils/async-save-text.js.map M static/maps/utils/localization.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map R static/scripts/base.js A static/scripts/bundled/analysis.bundled.js A static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/libs.bundled.js A static/scripts/bundled/libs.bundled.js.map A static/scripts/bundled/login.bundled.js A static/scripts/bundled/login.bundled.js.map R static/scripts/galaxy-app-base.js R static/scripts/galaxy.autocom_tagging.js R static/scripts/galaxy.base.js R static/scripts/galaxy.frame.js A static/scripts/galaxy.js M static/scripts/galaxy.library.js R static/scripts/galaxy.masthead.js M static/scripts/galaxy.menu.js M static/scripts/galaxy.pages.js R static/scripts/galaxy.panels.js R static/scripts/galaxy.tools.js R static/scripts/galaxy.ui.scrollPanel.js R static/scripts/galaxy.workflows.js A static/scripts/layout/masthead.js A static/scripts/layout/menu.js A static/scripts/layout/modal.js A static/scripts/layout/page.js A static/scripts/layout/panel.js A static/scripts/layout/scratchbook.js R static/scripts/libs/IE/IE7.js R static/scripts/libs/IE/IE8.js R static/scripts/libs/IE/blank.gif R static/scripts/libs/IE/excanvas.js R static/scripts/libs/IE/ie7-recalc.js A static/scripts/libs/backbone.js R static/scripts/libs/backbone/backbone.js A static/scripts/libs/bootstrap-tour.js A static/scripts/libs/common-libs.js R static/scripts/libs/handlebars.runtime.js A static/scripts/mvc/annotation.js R static/scripts/mvc/annotations.js R static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/app/app-login.js R static/scripts/mvc/app/app-view.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js R static/scripts/mvc/collection/collection-panel-edit.js R static/scripts/mvc/collection/collection-panel.js A static/scripts/mvc/collection/collection-view-edit.js A static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js R static/scripts/mvc/collection/paired-collection-creator.js R static/scripts/mvc/data.js A static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js R static/scripts/mvc/history/history-panel-annotated.js R static/scripts/mvc/history/history-panel-edit-current.js R static/scripts/mvc/history/history-panel-edit.js R static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-structure-view.js A static/scripts/mvc/history/history-view-annotated.js A static/scripts/mvc/history/history-view-edit-current.js A static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/list/list-item.js R static/scripts/mvc/list/list-panel.js A static/scripts/mvc/list/list-view.js A static/scripts/mvc/tag.js R static/scripts/mvc/tags.js A static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js A static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js A static/scripts/mvc/tours.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-ftp.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js A static/scripts/onload.js A static/scripts/polyfills.js R static/scripts/rgenetics/checkbox_and_radiobutton.js R static/scripts/rgenetics/helper_functions.js R static/scripts/rgenetics/timer.js R static/scripts/templates/compiled/panel_section.js R static/scripts/templates/compiled/tool_form.js R static/scripts/templates/compiled/tool_link.js R static/scripts/templates/compiled/tool_search.js R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js R static/scripts/tools/rgenetics/helper_functions.js R static/scripts/tools/rgenetics/timer.js A static/scripts/ui/autocom_tagging.js A static/scripts/ui/editable-text.js A static/scripts/ui/popupmenu.js A static/scripts/ui/scroll-panel.js M static/scripts/utils/ajax-queue.js A static/scripts/utils/async-save-text.js M static/scripts/utils/localization.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/style/blue/base.css A static/style/blue/bootstrap-tour.css R static/style/blue/galaxy.frame.masthead.css M static/style/blue/library.css M static/style/blue/masthead.css M templates/admin/reload_tool.mako R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako M templates/ind_share_base.mako A templates/js-app.mako M templates/refresh_frames.mako M templates/show_params.mako M templates/tagging_common.mako M templates/user/info.mako M templates/user/logout.mako M templates/user/username.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/copy.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/grid.mako A templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/history/share.mako A templates/webapps/galaxy/history/shared_grid.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako R templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/editor_generic_form.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/common.mako M test-data/3.bam M test/api/helpers.py M test/api/test_jobs.py M test/api/test_tools.py A test/api/test_tours.py A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/base/interactor.py M test/base/twilltestcase.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-anon-history-tests.js M test/casperjs/api-history-permission-tests.js M test/casperjs/api-tool-tests.js R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py M test/casperjs/modules/historyoptions.js M test/casperjs/modules/user.js M test/casperjs/registration-tests.js M test/casperjs/spaceghost.js M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/functional/test_admin_features.py M test/functional/test_data_security.py M test/functional/test_dataset_features.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_tags.py M test/functional/test_toolbox.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py A test/functional/tools/collection_type_source.xml A test/functional/tools/create_10.xml A test/functional/tools/empty_output.xml A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml A test/functional/tools/inputs_as_json.xml M test/functional/tools/maxseconds.xml M test/functional/tools/output_action_change_format.xml M test/functional/tools/output_format.xml M test/functional/tools/output_format_collection.xml A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml A test/functional/tools/validation_empty_dataset.xml M test/qunit/package.json M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js A test/qunit/tests/ui_tests.html A test/qunit/tests/ui_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py A test/tool_shed/functional/test_0540_get_all_metadata_from_api.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1085_repository_dependency_handling.py R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py A test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1130_datatype_converters.py A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1140_tool_help_images.py A test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1150_prior_installation_required.py R test/tool_shed/functional/test_1160_circular_prior_installation_required.py A test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_complex_prior_installation_required.py A test/tool_shed/functional/test_1170_prior_installation_required.py A test/tool_shed/functional/test_1180_circular_prior_installation_required.py A test/tool_shed/functional/test_1190_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py A test/tool_shed/test_data/0540_files/column_maker/column_maker.tar A test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml A test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar A test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml A test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py A test/unit/managers/test_HDCAManager.py A test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py A test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M test/unit/workflows/test_run_parameters.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/phenotype_association/linkToDavid.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py R tools/plotting/plot_filter.py R tools/plotting/plotter.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/sr_mapping/srma_wrapper.xml M tools/stats/aggregate_scores_in_intervals.py R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into csv_fix Commit: b8cb5432a204742956267ba5b76f6eb4804983b4 https://github.com/galaxyproject/galaxy/commit/b8cb5432a204742956267ba5b76f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/issue1818.tabular Log Message: ----------- Add test for #1818 to PR #1156. Commit: 5eb96a5fcf4ff8d521eeaa34172b5b72e902814b https://github.com/galaxyproject/galaxy/commit/5eb96a5fcf4ff8d521eeaa34172b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/grunt-tasks/style.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/tool_conf.xml.main M config/tool_data_table_conf.xml.sample M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init M create_db.sh A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/admin/framework_dependencies.rst M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/display_applications/application.py A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M manage_db.sh M manage_tools.sh M run.sh M run_reports.sh M run_tool_shed.sh M scripts/check_python.py M scripts/functional_tests.py M scripts/transfer.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tours.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/twilltestcase.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M test/unit/workflows/test_modules.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample M tools/data_source/upload.py Log Message: ----------- Merge PR #1156 into dev and fix #1818. Commit: 0029949ed2ead12735ce052aca328cc783139da6 https://github.com/galaxyproject/galaxy/commit/0029949ed2ead12735ce052aca32… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py Log Message: ----------- More fixups for specialized, more correct tabular datatypes. Followed through with @nsoranzo's comment: 1. overwrite CSV.sniff() and CSV.set_meta() methods with the ones from BaseCSV 2. remove BaseCSV class and rename CSV to BaseCSV 3. rename ExcelCSV class to CSV Also renamed ExcelTSV to TSV and corrected another bug in sample datatypes noticed by @nsoranzo. Commit: a85d6d556655bb3cc83270c41e9628488613600d https://github.com/galaxyproject/galaxy/commit/a85d6d556655bb3cc83270c41e96… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/issue1818.tabular Log Message: ----------- Merge pull request #1968 from jmchilton/csv_fix Improve tabular datatypes. Compare: https://github.com/galaxyproject/galaxy/compare/7129726e8fca...a85d6d556655

1 0

[galaxyproject/galaxy] cce822: make new beta TS tools installation via API config...
by GitHub 06 Apr '16

06 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cce822cfd6eb780ba7cd830d9c8206aa5c0d96ed https://github.com/galaxyproject/galaxy/commit/cce822cfd6eb780ba7cd830d9c82… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/webapps/galaxy/admin/index.mako Log Message: ----------- make new beta TS tools installation via API configurable we probably need more testing on Test/real Galaxies to rely on it fully Commit: 7129726e8fca56abe4c69271fbf89e9fa6813f6a https://github.com/galaxyproject/galaxy/commit/7129726e8fca56abe4c69271fbf8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Merge pull request #2088 from martenson/make-beta-install-config make new beta TS tools installation via API configurable Compare: https://github.com/galaxyproject/galaxy/compare/204627c9351b...7129726e8fca

1 0

[galaxyproject/usegalaxy-playbook] d668e2: Updates for Jetstream and fix IEs on Test (needed ...
by GitHub 06 Apr '16

06 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d668e2c384f1ad508b8ffc42548bb0f9df1dd769 https://github.com/galaxyproject/usegalaxy-playbook/commit/d668e2c384f1ad50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M .gitignore A files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_iu.yml A files/galaxy/test.galaxyproject.org/config/pulsar_jetstream_iu_actions.yml M roles/galaxyprojectdotorg.interactive_environments/README.md M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info M roles/galaxyprojectdotorg.interactive_environments/tasks/main.yml M roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml M roles/galaxyprojectdotorg.interactive_environments/tasks/webserver_conf.yml M roles/galaxyprojectdotorg.interactive_environments/templates/config.ini.j2 M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/supervisor/galaxy.j2 Log Message: ----------- Updates for Jetstream and fix IEs on Test (needed to support the allowed_images.yml config file)

1 0

[galaxyproject/galaxy] 99cb27: Fix reversed workflow upgrade message
by GitHub 06 Apr '16

06 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99cb27557ff66726fa3ffc578f80fe78422e5674 https://github.com/galaxyproject/galaxy/commit/99cb27557ff66726fa3ffc578f80… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix reversed workflow upgrade message Commit: 9b7be814b34494a4705cb19c44ce2039931f610f https://github.com/galaxyproject/galaxy/commit/9b7be814b34494a4705cb19c44ce… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py Log Message: ----------- Build tool lineage for versionless toolshed tool_ids The tool_id for a toolshed tool contains the version as last element (<toolshed>/<name>/<owner>/<id>/<version>). This means that looking up a tool lineage using a tools' tool_id does not work if the tool is installed in a different version than referenced by the tool_id. To allow this, we register the tool_lineage also under a tool_id that is stripped of the version. Commit: ab264ebeb4c0153e7c914df3e3f2c60d6ae149cb https://github.com/galaxyproject/galaxy/commit/ab264ebeb4c0153e7c914df3e3f2… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/lineages/factory.py Log Message: ----------- Remove version by slicing tool_id before last slash As pointed out by @nsoranzo, this may avoid conflicts when the version string appears more than once in tool_id. Commit: 204627c9351b6bce00bbe6c75a7fcc7d8f0f96c4 https://github.com/galaxyproject/galaxy/commit/204627c9351b6bce00bbe6c75a7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2082 from mvdbeek/tool_lineage_map tool lineage for versionless toolshed tool_ids Compare: https://github.com/galaxyproject/galaxy/compare/5523d8060fdf...204627c9351b

1 0