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

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[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

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[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

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[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

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[galaxyproject/galaxy] 9ecf99: make dependencies browsable again
by GitHub 08 Apr '16

08 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

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[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

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[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 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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 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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 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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 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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

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[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

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[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)

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[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

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