- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] be1025: Remove stray print statements.
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be10253b6947c8badfc71463d8331a1b53f5db9a https://github.com/galaxyproject/galaxy/commit/be10253b6947c8badfc71463d833… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py Log Message: ----------- Remove stray print statements. Not Python 3 compat. Commit: 0414c2628aa08d2303f6a50eb2cd556802ed416b https://github.com/galaxyproject/galaxy/commit/0414c2628aa08d2303f6a50eb2cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M .ci/py3_sources.txt Log Message: ----------- Expand PY3 linting to include another galaxy-lib module. Commit: 4c7f187b353d0a476e8c482b090538c7f8970606 https://github.com/galaxyproject/galaxy/commit/4c7f187b353d0a476e8c482b0905… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py Log Message: ----------- Merge pull request #2110 from jmchilton/remove_stray_prints galaxy-lib tweaks Compare: https://github.com/galaxyproject/galaxy/compare/2744d5541f7c...4c7f187b353d

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[galaxyproject/infrastructure-playbook] f2ae9a: Additional Jetstream fixes, launched what will hop...
by GitHub 08 Apr '16

08 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f2ae9af45bf403d15bc91af6bcf54f7fb13cc102 https://github.com/galaxyproject/infrastructure-playbook/commit/f2ae9af45bf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory A roles/cvmfs/defaults/main.yml R roles/cvmfs/vars/main.yml M roles/jetstream_nfs/vars/main.yml M roles/slurm/handlers/main.yml M roles/slurm/tasks/main.yml Log Message: ----------- Additional Jetstream fixes, launched what will hopefully be the first "real" node

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[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 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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 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

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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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[galaxyproject/galaxy] 974a9a: Add sample supervisor config
by GitHub 06 Apr '16

06 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 974a9adc1b16f54be1013cdd874dcfba5a352991 https://github.com/galaxyproject/galaxy/commit/974a9adc1b16f54be1013cdd874d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: A contrib/galaxy_supervisor.conf Log Message: ----------- Add sample supervisor config for galaxy served by uwsgi, with seperate handlers. Commit: 0de883271567f2acf59f77fe0bc69baa1adcf3ce https://github.com/galaxyproject/galaxy/commit/0de883271567f2acf59f77fe0bc6… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M contrib/galaxy_supervisor.conf Log Message: ----------- Change program name to galaxy_web Commit: 5523d8060fdfd5ef9792dadc41fa9af6118574d8 https://github.com/galaxyproject/galaxy/commit/5523d8060fdfd5ef9792dadc41fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: A contrib/galaxy_supervisor.conf Log Message: ----------- Merge pull request #2096 from mvdbeek/supervisor_uwsgi_contrib Add sample supervisor config Compare: https://github.com/galaxyproject/galaxy/compare/753b302df0fe...5523d8060fdf

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[galaxyproject/galaxy] 7cf0a8: Run external local set_metadata jobs in the job's ...
by GitHub 06 Apr '16

06 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7cf0a80d192ad876c46154d3996672a676c43fff https://github.com/galaxyproject/galaxy/commit/7cf0a80d192ad876c46154d39966… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Run external local set_metadata jobs in the job's working directory, because metadata temp files will be created in the cwd. Previously this would most likely be the Galaxy root directory, Which Was Bad. Commit: 753b302df0fef8eb6752968ef4371bc7c14e9ebc https://github.com/galaxyproject/galaxy/commit/753b302df0fef8eb6752968ef437… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #2094 from natefoo/local-set-meta Run external local set_metadata jobs in the job's working directory Compare: https://github.com/galaxyproject/galaxy/compare/4138860bfdaf...753b302df0fe

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[galaxyproject/infrastructure-playbook] da4c89: Buncha updates for Jetstream
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: da4c89f371b4c036cb2a26555fff60d711b95946 https://github.com/galaxyproject/infrastructure-playbook/commit/da4c89f371b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M ansible.cfg A galaxyenv/group_vars/cvmfsstratum1servers.yml M galaxyenv/inventory A jetstreamiuenv/files/slurm/launch A jetstreamiuenv/files/slurm/slurm.conf.elastic A jetstreamiuenv/files/slurm/terminate A jetstreamiuenv/group_vars/all.yml A jetstreamiuenv/group_vars/cvmfsclients.yml A jetstreamiuenv/group_vars/galaxynodes.yml A jetstreamiuenv/group_vars/slurmclients.yml A jetstreamiuenv/group_vars/slurmservers.yml A jetstreamiuenv/instance_inventory A jetstreamiuenv/inventory A jetstreamiuenv/launch.yml A jetstreamiuenv/playbook.yml A jetstreamiuenv/secret_group_vars/slurmclients.yml A jetstreamiuenv/templates/slurm/slurm.conf.j2 A jetstreamiuenv/terminate.yml M roles/cvmfs/handlers/main.yml M roles/cvmfs/tasks/client.yml M roles/cvmfs/tasks/localproxy.yml M roles/cvmfs/tasks/main.yml R roles/cvmfs/tasks/server.yml A roles/cvmfs/tasks/stratum1.yml R roles/cvmfs/templates/squid.conf.j2 A roles/cvmfs/templates/stratum1_squid.conf.j2 M roles/cvmfs/vars/main.yml A roles/jetstream_nfs/handlers/main.yml A roles/jetstream_nfs/tasks/main.yml A roles/jetstream_nfs/tasks/server.yml A roles/jetstream_nfs/vars/main.yml A roles/slurm/handlers/main.yml A roles/slurm/tasks/elastic.yml A roles/slurm/tasks/main.yml A roles/slurm/templates/slurmdbd.conf.j2 A roles/slurm/vars/debian.yml A roles/slurm/vars/redhat.yml A taccenv/group_vars/galaxynodes.yml M taccenv/playbook.yml Log Message: ----------- Buncha updates for Jetstream

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[galaxyproject/galaxy] 3b31f2: Fix deps.command.download_command on Mac OS X.
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b31f23eb6a69ea4e4a35e02745444910635da75 https://github.com/galaxyproject/galaxy/commit/3b31f23eb6a69ea4e4a35e027454… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Fix deps.command.download_command on Mac OS X. Previously -O- and --recursive would be used together - this doesn't seem to be possible on Mac OS X. See issue https://github.com/galaxyproject/planemo/issues/431. Commit: 4138860bfdaff9cf0fb4cdb0a7ea5068ddf1c5d7 https://github.com/galaxyproject/galaxy/commit/4138860bfdaff9cf0fb4cdb0a7ea… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge pull request #2075 from jmchilton/conda_download_fixes Fix deps.command.download_command on Mac OS X. Compare: https://github.com/galaxyproject/galaxy/compare/d6d216c92efb...4138860bfdaf

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[galaxyproject/galaxy] 53f178: Allow setting job_conf path for functional tests.
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 53f1782964d0fe447582d6f04a87ef0d6d8c5455 https://github.com/galaxyproject/galaxy/commit/53f1782964d0fe447582d6f04a87… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M run_tests.sh M test/base/driver_util.py Log Message: ----------- Allow setting job_conf path for functional tests. Commit: 7aa2d6840a8d0094c89a53cef06423701b677211 https://github.com/galaxyproject/galaxy/commit/7aa2d6840a8d0094c89a53cef064… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py A test/base/integration_util.py A test/integration/__init__.py A test/integration/embedded_pulsar_job_conf.xml A test/integration/test_pulsar_embedded.py Log Message: ----------- Implement IntegrationTestCase and EmbeddedPulsarTestCase. IntegrationTestCases differ from functional tests in that they start up a Galaxy instance configured on a per test class basis - so this new class of "integration tests" can test configuration modalities of Galaxy that cannot be tested with traditional Galaxy functional tests. Commit: 40e123b84b6825882f9172c212258e809bd73961 https://github.com/galaxyproject/galaxy/commit/40e123b84b6825882f9172c21225… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Fixup embedded Pulsar job runner based on @mvdbeek's comments. Commit: bdb41005c82678933656d651484cd1b9efeb55d1 https://github.com/galaxyproject/galaxy/commit/bdb41005c82678933656d651484c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix pulsar_conf/pulsar_config problem. One was being validated and the other was being read and documented. Commit: 2bd4de2025e55a9fc02ed3f74fbf297279e9d04f https://github.com/galaxyproject/galaxy/commit/2bd4de2025e55a9fc02ed3f74fbf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M test/integration/__init__.py M test/integration/embedded_pulsar_job_conf.xml Log Message: ----------- Fix things found by @mvdbeek Commit: d6d216c92efb973c9f03772fdab7ac51a3688692 https://github.com/galaxyproject/galaxy/commit/d6d216c92efb973c9f03772fdab7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M run_tests.sh M scripts/functional_tests.py M test/base/driver_util.py A test/base/integration_util.py A test/integration/__init__.py A test/integration/embedded_pulsar_job_conf.xml A test/integration/test_pulsar_embedded.py Log Message: ----------- Merge pull request #2078 from jmchilton/embed_dev Enhancements for Pulsar Embedded Runner Compare: https://github.com/galaxyproject/galaxy/compare/8d703e30a029...d6d216c92efb

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[galaxyproject/galaxy] a93532: Patch in visual separation of section parameters
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a935322d4db92a7a516276c77726ba482fbdc1a7 https://github.com/galaxyproject/galaxy/commit/a935322d4db92a7a516276c77726… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Patch in visual separation of section parameters Commit: 8d703e30a029c7531b8ff67ce8bf54eb1422b761 https://github.com/galaxyproject/galaxy/commit/8d703e30a029c7531b8ff67ce8bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2091 from erasche/fix_sections_001 Patch in visual separation of section parameters Compare: https://github.com/galaxyproject/galaxy/compare/118e2230276e...8d703e30a029

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[galaxyproject/galaxy] 2346b3: Fix job_wrapper.cleanup_job.
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2346b323315cc106745cc52b79f0a4fd2462e401 https://github.com/galaxyproject/galaxy/commit/2346b323315cc106745cc52b79f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix job_wrapper.cleanup_job. Broken in 16.04 with 81b5ca564ac7cdd855cb74dad8e98abc83a8efdc in PR #1688. Minor. Commit: 118e2230276ea582b136a84235813b8b582faf44 https://github.com/galaxyproject/galaxy/commit/118e2230276ea582b136a8423581… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #2089 from jmchilton/cleanup_job Fix job_wrapper.cleanup_job. Compare: https://github.com/galaxyproject/galaxy/compare/13af4a11a13c...118e2230276e

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[galaxyproject/galaxy] 2a53be: Show sections in workflow run
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 2a53be67ad4ac99b6e9fe5fb803bfa44442dbd3c https://github.com/galaxyproject/galaxy/commit/2a53be67ad4ac99b6e9fe5fb803b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Show sections in workflow run Commit: 3002e404ef17cd7db9b817085b2f3ed5a82bd109 https://github.com/galaxyproject/galaxy/commit/3002e404ef17cd7db9b817085b2f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Patch in visual separation of section parameters Commit: 040410b1d3f0ea01374f183ee0b9447e0fc3cefb https://github.com/galaxyproject/galaxy/commit/040410b1d3f0ea01374f183ee0b9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2092 from erasche/workflow-section-backport [16.01] Workflow section fix backport Compare: https://github.com/galaxyproject/galaxy/compare/65a7ebee2336...040410b1d3f0

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[galaxyproject/galaxy] 1114f4: Show sections in workflow run
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1114f476b65330388ab6f133756c2473c6835716 https://github.com/galaxyproject/galaxy/commit/1114f476b65330388ab6f133756c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Show sections in workflow run Commit: 13af4a11a13c3d8a12a49b29734d5df7bea5932a https://github.com/galaxyproject/galaxy/commit/13af4a11a13c3d8a12a49b29734d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2087 from guerler/fix_sections_000 Show sections in workflow run Compare: https://github.com/galaxyproject/galaxy/compare/e37761346625...13af4a11a13c

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[galaxyproject/galaxy] 3c8278: Implement new GIE proxy
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c8278c1bae103d5aaa3d264748c5f9049474dba https://github.com/galaxyproject/galaxy/commit/3c8278c1bae103d5aaa3d264748c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Implement new GIE proxy This provides an alternative proxy to the original NodeJS proxy. The implementation is done in golang, which has the nice property of compiling to a single binary. While it's a negative in terms of number of devteam who write that language, I'd argue it's not that much worse than nodejs in terms of accessibility. Features include: - Simple rest-ish API instead of file-based IPC - Automatic culling of containers, no more monitor_traffic.sh hacks - Admin configurable, cross GIE timeout setting Commit: 7830ee8724f488e1ea3efe49a8557aed74114811 https://github.com/galaxyproject/galaxy/commit/7830ee8724f488e1ea3efe49a855… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Address @mvdbeek's issues Commit: 5bfb87204841ddf566d078555e9f0458dd407de5 https://github.com/galaxyproject/galaxy/commit/5bfb87204841ddf566d078555e9f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Remove logging Commit: d7ed11477bbe50e4f058f389ebb753b412ac7000 https://github.com/galaxyproject/galaxy/commit/d7ed11477bbe50e4f058f389ebb7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Whitespace changes for travis Commit: 4c6cf5d4f9e2ecec8eb379ef8075ef20fb1da8fc https://github.com/galaxyproject/galaxy/commit/4c6cf5d4f9e2ecec8eb379ef8075… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Typo in config causes first run to fail Commit: e37761346625aed03af3bdee337686b0e697fd7a https://github.com/galaxyproject/galaxy/commit/e37761346625aed03af3bdee3376… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge pull request #1807 from erasche/gie-go-proxy-2 Implement new GIE proxy Compare: https://github.com/galaxyproject/galaxy/compare/1543f0d92507...e37761346625

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[galaxyproject/galaxy] 8b121a: Improve logging message in output_collect.
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b121ae31ca94c1c2a2c59b7f77da9c8097d2fa0 https://github.com/galaxyproject/galaxy/commit/8b121ae31ca94c1c2a2c59b7f77d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Improve logging message in output_collect. Conflicts: lib/galaxy/tools/parameters/output_collect.py Commit: 7c31a792fcdda60128848a53e9f567a99edb5c4a https://github.com/galaxyproject/galaxy/commit/7c31a792fcdda60128848a53e9f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow add_datasets to use optimized even if quota is used... Commit: ac14ad0897d4abb7875ad16a49dda7b6a43e3c84 https://github.com/galaxyproject/galaxy/commit/ac14ad0897d4abb7875ad16a49dd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Optimization for discovering datasets for dynamic output collection. Batch up job creation and adding datasets to the history in order to eliminate a bunch of database flushes. Using the create_input_collection tool from PR #1958 to create an output collection with 100 elements - the optimization reduces the job finish time from 45 seconds to 15 seconds. Before: ``` galaxy.jobs DEBUG 2016-03-21 01:51:01,377 job 24 ended (finish() executed in (15474.472 ms)) ``` After: ``` galaxy.jobs DEBUG 2016-03-21 01:50:06,659 job 23 ended (finish() executed in (46430.736 ms)) ``` Commit: 1543f0d925075ca1058e7bca48361a97be9bd557 https://github.com/galaxyproject/galaxy/commit/1543f0d925075ca1058e7bca4836… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #1959 from jmchilton/optimize_dataset_collection_discovery Optimization for discovering datasets for dynamic output collection. Compare: https://github.com/galaxyproject/galaxy/compare/497cd024da56...1543f0d92507

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[galaxyproject/galaxy] 89e6a3: Add IUC as a new default bioconda channel
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89e6a37d43d85ffd46a786e689e5b2fdc6a6c4ae https://github.com/galaxyproject/galaxy/commit/89e6a37d43d85ffd46a786e689e5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add IUC as a new default bioconda channel Commit: 497cd024da56f756fd73d31d68b462ac4aee77e9 https://github.com/galaxyproject/galaxy/commit/497cd024da56f756fd73d31d68b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #1950 from galaxyproject/iuc_default_conda_channel Add IUC as a new default bioconda channel Compare: https://github.com/galaxyproject/galaxy/compare/6bd8aff0b51f...497cd024da56

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[galaxyproject/galaxy] 9f2e0a: Add new generic GIE launcher
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9f2e0a4c25e4bf3b4658b45f3967d53273e0675d https://github.com/galaxyproject/galaxy/commit/9f2e0a4c25e4bf3b4658b45f3967… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: A config/plugins/interactive_environments/ipython/config/allowed_images.ini.sample A config/plugins/interactive_environments/rstudio/config/allowed_images.ini.sample A config/plugins/visualizations/gie-launcher/config/gie-launcher.xml A config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Add new generic GIE launcher Commit: 5e9a93dc9a14685225d5924b27b2c1c984e654bf https://github.com/galaxyproject/galaxy/commit/5e9a93dc9a14685225d5924b27b2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Rename based on updated allowed_images spec Commit: 43b646ccdf8ebc164c0da3f9a5e7bd3b4bfa184e https://github.com/galaxyproject/galaxy/commit/43b646ccdf8ebc164c0da3f9a5e7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/allowed_images.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Update config files Commit: 70de48d157bf278db80a71341ccb34ff4baadf63 https://github.com/galaxyproject/galaxy/commit/70de48d157bf278db80a71341ccb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/gie-launcher/templates/generic.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Update GIE mako files to handle new image stuff Commit: 170e2652cec0ec9c78bbb62e63aa5a3ddae52d2c https://github.com/galaxyproject/galaxy/commit/170e2652cec0ec9c78bbb62e63aa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Whitespace Commit: 70375af7f4e1552392e71fcc25bd0fd6d6de8279 https://github.com/galaxyproject/galaxy/commit/70375af7f4e1552392e71fcc25bd… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Correct ini->txt, better menu formatting Commit: f7d92e3fc69ef4a243dd928e9ce353ae6ed7cb7f https://github.com/galaxyproject/galaxy/commit/f7d92e3fc69ef4a243dd928e9ce3… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: A config/plugins/interactive_environments/bam_iobio/config/allowed_images.txt.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample R config/plugins/interactive_environments/ipython/config/allowed_images.ini.sample A config/plugins/interactive_environments/ipython/config/allowed_images.txt.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample R config/plugins/interactive_environments/rstudio/config/allowed_images.ini.sample A config/plugins/interactive_environments/rstudio/config/allowed_images.txt.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- More renames, add bam_iobio Commit: a326ce6a6fff086bd95db6a4d24cf595ec7ac1e7 https://github.com/galaxyproject/galaxy/commit/a326ce6a6fff086bd95db6a4d24c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Last ini->txt Commit: afe26640234ccc39d168c68f2216913a1ce0e268 https://github.com/galaxyproject/galaxy/commit/afe26640234ccc39d168c68f2216… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/gie-launcher/templates/generic.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Handle incoming additional_dataset_ids Commit: e32fa927232f029aa2f6fb822349f15f46a915ed https://github.com/galaxyproject/galaxy/commit/e32fa927232f029aa2f6fb822349… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/config/gie-launcher.xml Log Message: ----------- More datatypes Commit: 8fbe7ff2b0a4f3acde8f19823f40b3319dcba371 https://github.com/galaxyproject/galaxy/commit/8fbe7ff2b0a4f3acde8f19823f40… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Remove debugging statement Commit: fe0702e5bdc6843444e7cf1d186fb8efee155e5f https://github.com/galaxyproject/galaxy/commit/fe0702e5bdc6843444e7cf1d186f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Nicer help text Commit: 6c2305099f3826a21bf558eb8d57c33854fe57f8 https://github.com/galaxyproject/galaxy/commit/6c2305099f3826a21bf558eb8d57… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: A config/plugins/interactive_environments/jupyter/config/allowed_images.txt.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample Log Message: ----------- Adjust jupyter to support new spec Commit: 3410dad5b1c526ff153fd0e8fd27ac7790fe0502 https://github.com/galaxyproject/galaxy/commit/3410dad5b1c526ff153fd0e8fd27… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/jupyter/templates/jupyter.mako Log Message: ----------- Update jupyter launch command Commit: 29b984ea404fd0038bebc674b72d60784523a2e2 https://github.com/galaxyproject/galaxy/commit/29b984ea404fd0038bebc674b72d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Document launch command Commit: 7a0f74af2a03f8f18d92f5212cea0c203a6340dd https://github.com/galaxyproject/galaxy/commit/7a0f74af2a03f8f18d92f5212cea… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Make travis happy Commit: eaf758805af03811b09d86459697855ed3e3230a https://github.com/galaxyproject/galaxy/commit/eaf758805af03811b09d86459697… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/bam_iobio/config/allowed_images.txt.sample Log Message: ----------- Correct allowed_images file for bam iobio Commit: 6155d2768d24809c0f5bbb1e5cc402ec5e55054c https://github.com/galaxyproject/galaxy/commit/6155d2768d24809c0f5bbb1e5cc4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.txt.sample Log Message: ----------- Correct allowed_images file for jupyter Commit: 9192c115836a6f0f534847fcdc1297636442cbe2 https://github.com/galaxyproject/galaxy/commit/9192c115836a6f0f534847fcdc12… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako Log Message: ----------- Revert bam iobio Commit: 55bde3867250798b612568559d2b3a08480d4c65 https://github.com/galaxyproject/galaxy/commit/55bde3867250798b612568559d2b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: R config/plugins/interactive_environments/bam_iobio/config/allowed_images.txt.sample M config/plugins/interactive_environments/ipython/config/allowed_images.txt.sample M config/plugins/interactive_environments/jupyter/config/allowed_images.txt.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.txt.sample Log Message: ----------- Add textual descriptions to each image Commit: 69fc2f611208dd440e12f6dceea7cd0879972f5e https://github.com/galaxyproject/galaxy/commit/69fc2f611208dd440e12f6dceea7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Support image descriptions Commit: d9be7fbda7944dc8b9f722c5df8fa95c5885c26a https://github.com/galaxyproject/galaxy/commit/d9be7fbda7944dc8b9f722c5df8f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: R config/plugins/interactive_environments/ipython/config/allowed_images.txt.sample A config/plugins/interactive_environments/ipython/config/allowed_images.yml.sample R config/plugins/interactive_environments/jupyter/config/allowed_images.txt.sample A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample R config/plugins/interactive_environments/rstudio/config/allowed_images.txt.sample A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample Log Message: ----------- Reformat txt to yml files Commit: 351b28d46dfb08fc9e8e6646254b7fc0ca828512 https://github.com/galaxyproject/galaxy/commit/351b28d46dfb08fc9e8e6646254b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M .gitignore Log Message: ----------- Stop ignoring plugins in config Commit: 7d81e2014cba0ba21ef6cdde761bf3c38b3681fb https://github.com/galaxyproject/galaxy/commit/7d81e2014cba0ba21ef6cdde761b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M .gitignore Log Message: ----------- However, do keep ignoring locally adjusted confs Commit: c67cbe7e2717fd1b41b606d70fbf2dff7c2fd73d https://github.com/galaxyproject/galaxy/commit/c67cbe7e2717fd1b41b606d70fbf… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Reconfigure plugin for yaml Commit: 4414b8acbd896cf52e0a9c8f6a51fe25786f19a7 https://github.com/galaxyproject/galaxy/commit/4414b8acbd896cf52e0a9c8f6a51… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-27 (Sun, 27 Dec 2015) Changed paths: M config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Disallow newlines Commit: f29db6e30e4a06f5bb1f98c310606d226635b17c https://github.com/galaxyproject/galaxy/commit/f29db6e30e4a06f5bb1f98c31060… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Add button for GIEs Commit: 5a6d2361f7a74fd647881851766323bd606a4ddb https://github.com/galaxyproject/galaxy/commit/5a6d2361f7a74fd6478818517663… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: R config/plugins/visualizations/gie-launcher/config/gie-launcher.xml R config/plugins/visualizations/gie-launcher/templates/generic.mako Log Message: ----------- Remove custom viz plugin Commit: 590b75597edfec2833ede51b3c797dfe02edba3c https://github.com/galaxyproject/galaxy/commit/590b75597edfec2833ede51b3c79… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py A templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Move viz plugin into templates and lib Commit: 28172499d9ef2fbb3cb2f5bc5930c7f5049a0abd 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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 in master Commit: 05171a7bc5334d17988751cd52fb7b930566b599 https://github.com/galaxyproject/galaxy/commit/05171a7bc5334d17988751cd52fb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M static/scripts/layout/menu.js M templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Correct URL, fix compiled artefact Commit: 159d689b5eb41ef749ea4ddc264759710ee6f7bc https://github.com/galaxyproject/galaxy/commit/159d689b5eb41ef749ea4ddc2647… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Correctly launch with dataset_id Commit: 65beb5f4b3d9acfef3c1e224f2fb8ad805f02bcb https://github.com/galaxyproject/galaxy/commit/65beb5f4b3d9acfef3c1e224f2fb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Correct text on dataset selector, hide deleted Commit: 241335539d84aec270ba7ef6c41b7c2854535ebb https://github.com/galaxyproject/galaxy/commit/241335539d84aec270ba7ef6c41b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Make use of available methods, correct ID Commit: 4bf14db042adb771888662dd4d3cf1ceb74f5cf0 https://github.com/galaxyproject/galaxy/commit/4bf14db042adb771888662dd4d3c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Correct the format statement for mounting Commit: efcbfe6a0cc9fa882ea0e94fdf021de799993e0e https://github.com/galaxyproject/galaxy/commit/efcbfe6a0cc9fa882ea0e94fdf02… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Make flake8 happy Commit: cf4c1539df29ecd7e38c7ece351a1a31271dd170 https://github.com/galaxyproject/galaxy/commit/cf4c1539df29ecd7e38c7ece351a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Improved logic for determining if something is a GIE directory. Commit: 74eb31976318d8461bea0a0ad412f73faec00154 https://github.com/galaxyproject/galaxy/commit/74eb31976318d8461bea0a0ad412… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: R config/plugins/interactive_environments/ipython/config/allowed_images.yml.sample Log Message: ----------- Remove ipython config, GIE has been removed in 16.04. Commit: 877c925190915ad75072d568288a22b940dbd80f https://github.com/galaxyproject/galaxy/commit/877c925190915ad75072d568288a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fixup sample comments. Commit: be23cdb7190506ec03fb4bdc99b9fa9cab825bfd https://github.com/galaxyproject/galaxy/commit/be23cdb7190506ec03fb4bdc99b9… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: R config/plugins/interactive_environments/ipython/config/allowed_images.yml.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge pull request #13 from jmchilton/gie-generic-fixes Two fixes to gie generic stuff.. Commit: 95b31b63361c3140af2e8b170a764d8c1740fd15 https://github.com/galaxyproject/galaxy/commit/95b31b63361c3140af2e8b170a76… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #14 from jmchilton/gie-generic-fixes Fixup sample comments. Commit: fd28b812ef4bd8ec726a72f07d50998b35fb677c https://github.com/galaxyproject/galaxy/commit/fd28b812ef4bd8ec726a72f07d50… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Address @jmchilton's issue Commit: e62befe93b6896ab4c456e9bb5b21a47de3523f1 https://github.com/galaxyproject/galaxy/commit/e62befe93b6896ab4c456e9bb5b2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: R config/plugins/interactive_environments/ipython/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge remote-tracking branch 'origin/gie-generic' into 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scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py A scripts/patch.sh M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.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 M static/style/blue/base.css M test/tool_shed/base/twilltestcase.py M test/unit/test_objectstore.py A test/unit/tools/test_history_imp_exp.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini Log Message: ----------- Repack artefacts, merge dev Commit: 50770c962a3018c3b3a06f0b3faab0f9ed4d1d14 https://github.com/galaxyproject/galaxy/commit/50770c962a3018c3b3a06f0b3faa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M 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config/tool_conf.xml.main M create_db.sh M doc/source/admin/framework_dependencies.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.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/command_factory.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.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/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/managers/histories.py M 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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/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_1040_install_repository_basic_circular_dependencies.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M tools/data_source/upload.py Log Message: ----------- Merge in master Commit: 1c94fdd528ad540a1291015c044f131816d7368c https://github.com/galaxyproject/galaxy/commit/1c94fdd528ad540a1291015c044f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/workflow/modules.py M lib/tool_shed/tool_shed_registry.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.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/layout/menu.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/display.mako M test/base/twilltestcase.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/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_select_parameters.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge in master Commit: cc9aee6fc8b4b89e2aa318661dbc4381b8039077 https://github.com/galaxyproject/galaxy/commit/cc9aee6fc8b4b89e2aa318661dbc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix to gie-generic. Commit: 51e722468383ffcf2e63e2e1ff01b8a0beec6885 https://github.com/galaxyproject/galaxy/commit/51e722468383ffcf2e63e2e1ff01… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #15 from jmchilton/gie-generic A fix to my previous fix. Commit: aee38feeb4d3017cb1d0edc209bd1924c6a2cd32 https://github.com/galaxyproject/galaxy/commit/aee38feeb4d3017cb1d0edc209bd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M .gitignore M Makefile M README.rst M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.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 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test/unit/tool_shed_unit_tests/test_tool_panel_manager.py A tool-data/biom_simple_display.loc.sample Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into gie-generic Conflicts: static/maps/layout/menu.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/layout/menu.js Commit: 6bd8aff0b51ffbe07eef14d871da08fb0b76267e https://github.com/galaxyproject/galaxy/commit/6bd8aff0b51ffbe07eef14d871da… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/layout/menu.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/layout/menu.js A templates/webapps/galaxy/visualization/gie.mako Log Message: ----------- Merge pull request #1403 from erasche/gie-generic Generic GIE Launcher, GIE Image Chooser, multiple datasets Compare: https://github.com/galaxyproject/galaxy/compare/3bd802268dc4...6bd8aff0b51f

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