- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 9efcfd: Update README.rst
by GitHub 30 Mar '18

30 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9efcfd462dcb3e9dd78d088ff15e753cbc2f9dde https://github.com/galaxyproject/galaxy/commit/9efcfd462dcb3e9dd78d088ff15e… Author: Jennifer Hillman-Jackson <jennaj(a)users.noreply.github.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M README.rst Log Message: ----------- Update README.rst Updated Roadmap link Commit: ac74b7ffb2215b3f73997a760a15b26f39e64d3b https://github.com/galaxyproject/galaxy/commit/ac74b7ffb2215b3f73997a760a15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M README.rst Log Message: ----------- Merge pull request #5815 from jennaj/jennaj-readme-edit Update README.rst Compare: https://github.com/galaxyproject/galaxy/compare/08c2c5b5ac7a...ac74b7ffb221

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[galaxyproject/galaxy]
by GitHub 30 Mar '18

30 Mar '18

Branch: refs/heads/jennaj-readme-edit Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 7b50fd: Updated Roadmap link in README.rst
by GitHub 30 Mar '18

30 Mar '18

Branch: refs/heads/jennaj-readme-edit Home: https://github.com/galaxyproject/galaxy Commit: 7b50fd614d73838674b987144e784e2824d5c39f https://github.com/galaxyproject/galaxy/commit/7b50fd614d73838674b987144e78… Author: Jennifer Hillman-Jackson <jennaj(a)users.noreply.github.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M README.rst Log Message: ----------- Updated Roadmap link in README.rst

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[galaxyproject/usegalaxy-playbook] 8323fc: Update Main
by GitHub 29 Mar '18

29 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8323fc94564e86ea2e72568552ba3a04465850f6 https://github.com/galaxyproject/usegalaxy-playbook/commit/8323fc94564e86ea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] c99c7b: Fix type of some options in config_schema.yml
by GitHub 29 Mar '18

29 Mar '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: c99c7b4d842b844677673472b9aa2b13e4123aeb https://github.com/galaxyproject/galaxy/commit/c99c7b4d842b844677673472b9aa… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix type of some options in config_schema.yml Also: - drop unused `nginx_x_archive_files_base` option, last use removed in commit fe5983aafca1fae0b60ed16838799b58f4aca11c - rebuild config samples and docs. Commit: 80ac55b3ff132cf6e1778b99cb6ffb01bec9cfe8 https://github.com/galaxyproject/galaxy/commit/80ac55b3ff132cf6e1778b99cb6f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Don't quote ints in .ini to .yml config conversion Commit: 1b13bfa48e1b3e805a46feec55a3c698ce1fa524 https://github.com/galaxyproject/galaxy/commit/1b13bfa48e1b3e805a46feec55a3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Log the pid of the first uWSGI process So it is the same that gets written to file when using the `--pidfile` option of `uwsgi`. Commit: 8fa8660b25dccf62a045597bee03441b5b68b71b https://github.com/galaxyproject/galaxy/commit/8fa8660b25dccf62a045597bee03… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/hash_util.py M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Small improvements to scripts/grt/export.py for testing. - Don't rely on external sha256sum, use Python hashing (add utility to hash_util to enable this). - Drop unused galaxy_config from grt.yml.sample - it isn't used anywhere as far as I can tell. Commit: 5f3f792f6f4ba67a2dd49e9c69b28567540c2c48 https://github.com/galaxyproject/galaxy/commit/5f3f792f6f4ba67a2dd49e9c69b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/communication/communication_server.py M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py A test/integration/test_scripts.py Log Message: ----------- Unification of Galaxy configuration parsing for scripts/* Commit: 16d821e12e53655947a6859a221b19a8d05eb2c4 https://github.com/galaxyproject/galaxy/commit/16d821e12e53655947a6859a221b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/sync_reports_config.py M scripts/transfer.py Log Message: ----------- Mark scripts/* that don't work with YAML configuraiton options as deprecated. Commit: 1911a55390eb4c6f9c7beb69b8f364ff6b76a119 https://github.com/galaxyproject/galaxy/commit/1911a55390eb4c6f9c7beb69b8f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh Log Message: ----------- Remove unused and unuseful scripts. Commit: 49fed72eeab48cda9e962f2d1a678825f40842b2 https://github.com/galaxyproject/galaxy/commit/49fed72eeab48cda9e962f2d1a67… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh Log Message: ----------- Drop data library whoosh/lucene scripts. We don't set that config option in Galaxy anymore so these are broken anyway. Commit: fea7953410a4145f45afbe1656735febcf390a92 https://github.com/galaxyproject/galaxy/commit/fea7953410a4145f45afbe165673… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py Log Message: ----------- Remove two scripts - dataset purging hasn't worked this way for a very long time. Commit: b14928d97203d4d459c289c393589e4f4120e3e4 https://github.com/galaxyproject/galaxy/commit/b14928d97203d4d459c289c39358… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Cleanup script integration tests. Commit: 14e98becfe9c4d76677d9a9d0bc568c75f242bf2 https://github.com/galaxyproject/galaxy/commit/14e98becfe9c4d76677d9a9d0bc5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Cleanup incorrect FIXME - spotted by @nsoranzo. Commit: a177173672b86f4da8f83c3068dcb63f5f49cc40 https://github.com/galaxyproject/galaxy/commit/a177173672b86f4da8f83c3068dc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Fix missing ENV information in config parameter args. Commit: 8fb6aa5860344cf80c18b8fef43b43b26856ec2a https://github.com/galaxyproject/galaxy/commit/8fb6aa5860344cf80c18b8fef43b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Bring in @nsoranzo's requested changes for config_file_from_args, etc. Commit: bb90ae93d810cd829ef026a3d086d51c11ac5394 https://github.com/galaxyproject/galaxy/commit/bb90ae93d810cd829ef026a3d086… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/grt/export.py M scripts/grt/upload.py M test/integration/test_scripts.py Log Message: ----------- More grt fixes - spotted by @nsoranzo. Commit: a1f0e1772ec5280a0523f2218008933f768e886e https://github.com/galaxyproject/galaxy/commit/a1f0e1772ec5280a0523f2218008… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Redact help for --config-section option for @nsoranzo. Kept the string in the file for in-code documentation but hiding it from users. Commit: 04a901771b59d1fcf8070cd4c4de1f464e304e55 https://github.com/galaxyproject/galaxy/commit/04a901771b59d1fcf8070cd4c4de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- [18.01] Fix SQL query for "workflows shared with me" as part of workflow index. Before and after queries here: https://gist.github.com/jmchilton/dc57bca60178341d9ce0f6cf6d4bd36f You can see that before the joined load of the stored workflow wasn't being registered by SQLalchemy properly and so it was joining that table twice - once using the proper index and another time just walking the whole table. The filter and order by were being applied to the unconditional version - kind of like saying give me all the workflows and the right workflows and I will check all the workflows to see if this one is deleted instead of just the subset of workflows that are actually being shared with the target user. Commit: ff0f0b611282fb0c4c5742c034f7cef0ec86f475 https://github.com/galaxyproject/galaxy/commit/ff0f0b611282fb0c4c5742c034f7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py Log Message: ----------- Fix model operations that produce datasets for 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03 Should only affect unzip I think - fixes #5780 - probably need to rebuild collections though, collections built in the meantime are going to be broken in the DB. Includes test case that fails against 18.01. Commit: 3876f12e7d3ce7ec73d14ae99f06edae01020412 https://github.com/galaxyproject/galaxy/commit/3876f12e7d3ce7ec73d14ae99f06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5784 from jmchilton/1801_fix_unzip [18.01] Fix model operation tools that produce standalone datasets. Commit: fbb47f6e03d0ca9190e3f665515ba45ac64e14ce https://github.com/galaxyproject/galaxy/commit/fbb47f6e03d0ca9190e3f665515b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5745 from nsoranzo/release_18.01_fix_config [18.01] Configuration fixes Commit: 62d4582ef6913a4c681db2a08369a7757523de42 https://github.com/galaxyproject/galaxy/commit/62d4582ef6913a4c681db2a08369… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py Log Message: ----------- Touch up script unification PR based on @natefoo comments. Commit: d6be56256fcbee53509dc867d863819621ef1d08 https://github.com/galaxyproject/galaxy/commit/d6be56256fcbee53509dc867d863… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #5782 from jmchilton/fix_1801 [18.01] Fix SQL query for "workflows shared with me" as part of workflow index. Commit: 4d742c3b1316aa808201c5bf3faec2587c345590 https://github.com/galaxyproject/galaxy/commit/4d742c3b1316aa808201c5bf3fae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M Makefile M client/README.md Log Message: ----------- Clarify make targets, update client/README Commit: b960260a3449a23dc35a0f126de41c37276d8cfd https://github.com/galaxyproject/galaxy/commit/b960260a3449a23dc35a0f126de4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Mention the client README specifically in CONTRIBUTING, to make it more obvious. Commit: d61268cc6d58a5fbecc0399a7fe8087be45d4861 https://github.com/galaxyproject/galaxy/commit/d61268cc6d58a5fbecc0399a7fe8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Articles are important. Commit: cbd7cb3cbcc93ef9abd651fff0760a91b5624127 https://github.com/galaxyproject/galaxy/commit/cbd7cb3cbcc93ef9abd651fff076… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Reflow text Commit: 05584244a7a5fb8790c513d6e451ac629b2f2955 https://github.com/galaxyproject/galaxy/commit/05584244a7a5fb8790c513d6e451… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Drop old bitbucket/galaxy/galaxy-dist reference. Commit: c6ae97edaef3a146955731aefe510887f4c8b6d0 https://github.com/galaxyproject/galaxy/commit/c6ae97edaef3a146955731aefe51… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge pull request #5774 from nsoranzo/release_18.01_fix_pid [18.01] Log the pid of the first uWSGI process Commit: 96d9d0e5a236eb3fc7cf6f6612d82915fa5790e8 https://github.com/galaxyproject/galaxy/commit/96d9d0e5a236eb3fc7cf6f6612d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Better re-use of `tool` attribute Commit: 4f870490f2d289b2921c422ff66e92ee5decb352 https://github.com/galaxyproject/galaxy/commit/4f870490f2d289b2921c422ff66e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Simplify get_datatype_by_extension() method Commit: 334aea3adc975793d215f1622efc892718ecad75 https://github.com/galaxyproject/galaxy/commit/334aea3adc975793d215f1622efc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Erase trello from Contributing. Commit: 7d394d243b7d041ab357a0279e4920ab4a03fe7b https://github.com/galaxyproject/galaxy/commit/7d394d243b7d041ab357a0279e49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M client/README.md Log Message: ----------- Proofreading - thanks @nsoranzo Commit: d53cbe3538f186da903726ac1d00630e94cfe894 https://github.com/galaxyproject/galaxy/commit/d53cbe3538f186da903726ac1d00… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M Makefile M client/README.md Log Message: ----------- Merge pull request #5800 from dannon/client_readme_clarifications [18.01] Client related readme/makefile clarifications Commit: 288d13b60681a3729fd38c09b41763b520239317 https://github.com/galaxyproject/galaxy/commit/288d13b60681a3729fd38c09b417… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix metadata setting for CRAM files Should fix https://github.com/galaxyproject/galaxy/issues/5801. Commit: 7e5a90cc1fd5de729e416dd249f92621f883cce8 https://github.com/galaxyproject/galaxy/commit/7e5a90cc1fd5de729e416dd249f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Use app.datatypes_registry in ValidationContext.from_app() Commit: d5baea1dfc1998bcba5a0083b6b94769455bc247 https://github.com/galaxyproject/galaxy/commit/d5baea1dfc1998bcba5a0083b6b9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Handle an empty datatypes_registry Also transform it to an object attribute for re-use. Commit: 2c4bf95c3c5416f381cd8aea210f66ffef43498d https://github.com/galaxyproject/galaxy/commit/2c4bf95c3c5416f381cd8aea210f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5806 from nsoranzo/release_18.01_ValidationContext_fixes [18.01] Use app.datatypes_registry in ValidationContext.from_app() Commit: 241fadc98159f206b26938ba5626c1f24b1120c2 https://github.com/galaxyproject/galaxy/commit/241fadc98159f206b26938ba5626… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5805 from mvdbeek/fix_cram_metadata [18.01] Fix metadata setting for CRAM files Commit: 009921387dc3f2ea0731e82fe137c7b8d06f7e8a https://github.com/galaxyproject/galaxy/commit/009921387dc3f2ea0731e82fe137… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test/integration/test_scripts.py Log Message: ----------- Merge pull request #5769 from jmchilton/unify_scripts [18.01] Fix scripts/ for YAML/ENV configuration processing Commit: c5095d1634a95ebc3ee3d1108984acbcd746a603 https://github.com/galaxyproject/galaxy/commit/c5095d1634a95ebc3ee3d1108984… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M CONTRIBUTING.md M Makefile M client/README.md M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py M test/api/test_tools.py A test/integration/test_scripts.py Log Message: ----------- Merge branch 'release_18.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/5d0d66e7289d...c5095d1634a9

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[galaxyproject/galaxy] 8fa866: Small improvements to scripts/grt/export.py for te...
by GitHub 29 Mar '18

29 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8fa8660b25dccf62a045597bee03441b5b68b71b https://github.com/galaxyproject/galaxy/commit/8fa8660b25dccf62a045597bee03… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/hash_util.py M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Small improvements to scripts/grt/export.py for testing. - Don't rely on external sha256sum, use Python hashing (add utility to hash_util to enable this). - Drop unused galaxy_config from grt.yml.sample - it isn't used anywhere as far as I can tell. Commit: 5f3f792f6f4ba67a2dd49e9c69b28567540c2c48 https://github.com/galaxyproject/galaxy/commit/5f3f792f6f4ba67a2dd49e9c69b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/communication/communication_server.py M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py A test/integration/test_scripts.py Log Message: ----------- Unification of Galaxy configuration parsing for scripts/* Commit: 16d821e12e53655947a6859a221b19a8d05eb2c4 https://github.com/galaxyproject/galaxy/commit/16d821e12e53655947a6859a221b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/sync_reports_config.py M scripts/transfer.py Log Message: ----------- Mark scripts/* that don't work with YAML configuraiton options as deprecated. Commit: 1911a55390eb4c6f9c7beb69b8f364ff6b76a119 https://github.com/galaxyproject/galaxy/commit/1911a55390eb4c6f9c7beb69b8f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh Log Message: ----------- Remove unused and unuseful scripts. Commit: 49fed72eeab48cda9e962f2d1a678825f40842b2 https://github.com/galaxyproject/galaxy/commit/49fed72eeab48cda9e962f2d1a67… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh Log Message: ----------- Drop data library whoosh/lucene scripts. We don't set that config option in Galaxy anymore so these are broken anyway. Commit: fea7953410a4145f45afbe1656735febcf390a92 https://github.com/galaxyproject/galaxy/commit/fea7953410a4145f45afbe165673… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py Log Message: ----------- Remove two scripts - dataset purging hasn't worked this way for a very long time. Commit: b14928d97203d4d459c289c393589e4f4120e3e4 https://github.com/galaxyproject/galaxy/commit/b14928d97203d4d459c289c39358… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Cleanup script integration tests. Commit: 14e98becfe9c4d76677d9a9d0bc568c75f242bf2 https://github.com/galaxyproject/galaxy/commit/14e98becfe9c4d76677d9a9d0bc5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Cleanup incorrect FIXME - spotted by @nsoranzo. Commit: a177173672b86f4da8f83c3068dcb63f5f49cc40 https://github.com/galaxyproject/galaxy/commit/a177173672b86f4da8f83c3068dc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Fix missing ENV information in config parameter args. Commit: 8fb6aa5860344cf80c18b8fef43b43b26856ec2a https://github.com/galaxyproject/galaxy/commit/8fb6aa5860344cf80c18b8fef43b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Bring in @nsoranzo's requested changes for config_file_from_args, etc. Commit: bb90ae93d810cd829ef026a3d086d51c11ac5394 https://github.com/galaxyproject/galaxy/commit/bb90ae93d810cd829ef026a3d086… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/grt/export.py M scripts/grt/upload.py M test/integration/test_scripts.py Log Message: ----------- More grt fixes - spotted by @nsoranzo. Commit: a1f0e1772ec5280a0523f2218008933f768e886e https://github.com/galaxyproject/galaxy/commit/a1f0e1772ec5280a0523f2218008… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/util/script.py Log Message: ----------- Redact help for --config-section option for @nsoranzo. Kept the string in the file for in-code documentation but hiding it from users. Commit: 62d4582ef6913a4c681db2a08369a7757523de42 https://github.com/galaxyproject/galaxy/commit/62d4582ef6913a4c681db2a08369… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py Log Message: ----------- Touch up script unification PR based on @natefoo comments. Commit: 009921387dc3f2ea0731e82fe137c7b8d06f7e8a https://github.com/galaxyproject/galaxy/commit/009921387dc3f2ea0731e82fe137… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test/integration/test_scripts.py Log Message: ----------- Merge pull request #5769 from jmchilton/unify_scripts [18.01] Fix scripts/ for YAML/ENV configuration processing Compare: https://github.com/galaxyproject/galaxy/compare/241fadc98159...009921387dc3

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[galaxyproject/galaxy] 1774c7: Bump psycopg2 to 2.7.4; this fixes compatibility w...
by GitHub 29 Mar '18

29 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1774c7742ab97652e1e5e8c356d686110b947a5e https://github.com/galaxyproject/galaxy/commit/1774c7742ab97652e1e5e8c356d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Bump psycopg2 to 2.7.4; this fixes compatibility with the default ubuntu 18.04 postgresql Commit: 3b8471468e968e65ac74c8aa9564e7f5221af3ce https://github.com/galaxyproject/galaxy/commit/3b8471468e968e65ac74c8aa9564… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Per http://initd.org/psycopg/articles/2018/02/08/psycopg-274-released/, swap to psycopg2-binary package for 2.7.4 (and future) wheels. Commit: 3df781a55465ec32f79a17f66a373b7317b12fee https://github.com/galaxyproject/galaxy/commit/3df781a55465ec32f79a17f66a37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Update psycopg2 conditional dependency check to use the new psycopg2-binary package name. Commit: e84dd5db6b1eb924f4f6897103774152fc0e2cef https://github.com/galaxyproject/galaxy/commit/e84dd5db6b1eb924f4f689710377… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Rudimentary check for old psycopg2==2.4.3, which we clean up before installing psycopg2-binary. Commit: 30c2ea0c3e61db387e7c31ecb7fd18216c0e083e https://github.com/galaxyproject/galaxy/commit/30c2ea0c3e61db387e7c31ecb7fd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Make psycopg2 grep a little more robust Commit: d44b47741ba6e2fd670a150f7d35fb3e8cdb56a9 https://github.com/galaxyproject/galaxy/commit/d44b47741ba6e2fd670a150f7d35… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Specify format to squelch deprecation warning about columns/legacy Commit: 8742614e5243c61ee15823c0cf8aa512e9bb026f https://github.com/galaxyproject/galaxy/commit/8742614e5243c61ee15823c0cf8a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Quieter grepping. Commit: 60ca4d4cc94966598c102ea5a473270ea15e9b22 https://github.com/galaxyproject/galaxy/commit/60ca4d4cc94966598c102ea5a473… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Instead of using -q, send to /dev/null, since the early pipe exit blows up pip Commit: 08c2c5b5ac7a8768a15a886cabed0fdc4963f37c https://github.com/galaxyproject/galaxy/commit/08c2c5b5ac7a8768a15a886cabed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #5698 from dannon/psycopg2_bump Bump psycopg2 to 2.7.4; Compare: https://github.com/galaxyproject/galaxy/compare/a85b8a83cbfe...08c2c5b5ac7a

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[galaxyproject/galaxy] 288d13: Fix metadata setting for CRAM files
by GitHub 29 Mar '18

29 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 288d13b60681a3729fd38c09b41763b520239317 https://github.com/galaxyproject/galaxy/commit/288d13b60681a3729fd38c09b417… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix metadata setting for CRAM files Should fix https://github.com/galaxyproject/galaxy/issues/5801. Commit: 241fadc98159f206b26938ba5626c1f24b1120c2 https://github.com/galaxyproject/galaxy/commit/241fadc98159f206b26938ba5626… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5805 from mvdbeek/fix_cram_metadata [18.01] Fix metadata setting for CRAM files Compare: https://github.com/galaxyproject/galaxy/compare/2c4bf95c3c54...241fadc98159

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[galaxyproject/galaxy] 96d9d0: Better re-use of `tool` attribute
by GitHub 29 Mar '18

29 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 96d9d0e5a236eb3fc7cf6f6612d82915fa5790e8 https://github.com/galaxyproject/galaxy/commit/96d9d0e5a236eb3fc7cf6f6612d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Better re-use of `tool` attribute Commit: 4f870490f2d289b2921c422ff66e92ee5decb352 https://github.com/galaxyproject/galaxy/commit/4f870490f2d289b2921c422ff66e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Simplify get_datatype_by_extension() method Commit: 7e5a90cc1fd5de729e416dd249f92621f883cce8 https://github.com/galaxyproject/galaxy/commit/7e5a90cc1fd5de729e416dd249f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Use app.datatypes_registry in ValidationContext.from_app() Commit: d5baea1dfc1998bcba5a0083b6b94769455bc247 https://github.com/galaxyproject/galaxy/commit/d5baea1dfc1998bcba5a0083b6b9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Handle an empty datatypes_registry Also transform it to an object attribute for re-use. Commit: 2c4bf95c3c5416f381cd8aea210f66ffef43498d https://github.com/galaxyproject/galaxy/commit/2c4bf95c3c5416f381cd8aea210f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5806 from nsoranzo/release_18.01_ValidationContext_fixes [18.01] Use app.datatypes_registry in ValidationContext.from_app() Compare: https://github.com/galaxyproject/galaxy/compare/d53cbe3538f1...2c4bf95c3c54

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[galaxyproject/galaxy] 4d742c: Clarify make targets, update client/README
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 4d742c3b1316aa808201c5bf3faec2587c345590 https://github.com/galaxyproject/galaxy/commit/4d742c3b1316aa808201c5bf3fae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M Makefile M client/README.md Log Message: ----------- Clarify make targets, update client/README Commit: b960260a3449a23dc35a0f126de41c37276d8cfd https://github.com/galaxyproject/galaxy/commit/b960260a3449a23dc35a0f126de4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Mention the client README specifically in CONTRIBUTING, to make it more obvious. Commit: d61268cc6d58a5fbecc0399a7fe8087be45d4861 https://github.com/galaxyproject/galaxy/commit/d61268cc6d58a5fbecc0399a7fe8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Articles are important. Commit: cbd7cb3cbcc93ef9abd651fff0760a91b5624127 https://github.com/galaxyproject/galaxy/commit/cbd7cb3cbcc93ef9abd651fff076… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Reflow text Commit: 05584244a7a5fb8790c513d6e451ac629b2f2955 https://github.com/galaxyproject/galaxy/commit/05584244a7a5fb8790c513d6e451… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Drop old bitbucket/galaxy/galaxy-dist reference. Commit: 334aea3adc975793d215f1622efc892718ecad75 https://github.com/galaxyproject/galaxy/commit/334aea3adc975793d215f1622efc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md Log Message: ----------- Erase trello from Contributing. Commit: 7d394d243b7d041ab357a0279e4920ab4a03fe7b https://github.com/galaxyproject/galaxy/commit/7d394d243b7d041ab357a0279e49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M client/README.md Log Message: ----------- Proofreading - thanks @nsoranzo Commit: d53cbe3538f186da903726ac1d00630e94cfe894 https://github.com/galaxyproject/galaxy/commit/d53cbe3538f186da903726ac1d00… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M CONTRIBUTING.md M Makefile M client/README.md Log Message: ----------- Merge pull request #5800 from dannon/client_readme_clarifications [18.01] Client related readme/makefile clarifications Compare: https://github.com/galaxyproject/galaxy/compare/c6ae97edaef3...d53cbe3538f1

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[galaxyproject/usegalaxy-playbook] f6d161: Upgraded prokka to version 1.13
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f6d1619f1fc1e85d21d51edea8da5ef8c2bfa031 https://github.com/galaxyproject/usegalaxy-playbook/commit/f6d1619f1fc1e85d… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Upgraded prokka to version 1.13

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[galaxyproject/galaxy] 0a1ccd: Lock pysam to 0.14.1 in Pipfile.
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a1ccdba1275948e71cd4e2da86a182c2cb7a7eb https://github.com/galaxyproject/galaxy/commit/0a1ccdba1275948e71cd4e2da86a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile Log Message: ----------- Lock pysam to 0.14.1 in Pipfile. Commit: a85b8a83cbfeb6aaba1b3e6d86f3ae737f369ed3 https://github.com/galaxyproject/galaxy/commit/a85b8a83cbfeb6aaba1b3e6d86f3… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile Log Message: ----------- Merge pull request #5798 from dannon/lock_pysam Lock pysam to 0.14.1 in Pipfile. Compare: https://github.com/galaxyproject/galaxy/compare/0ff93b0e537c...a85b8a83cbfe

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[galaxyproject/galaxy] 1b13bf: Log the pid of the first uWSGI process
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1b13bfa48e1b3e805a46feec55a3c698ce1fa524 https://github.com/galaxyproject/galaxy/commit/1b13bfa48e1b3e805a46feec55a3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Log the pid of the first uWSGI process So it is the same that gets written to file when using the `--pidfile` option of `uwsgi`. Commit: c6ae97edaef3a146955731aefe510887f4c8b6d0 https://github.com/galaxyproject/galaxy/commit/c6ae97edaef3a146955731aefe51… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge pull request #5774 from nsoranzo/release_18.01_fix_pid [18.01] Log the pid of the first uWSGI process Commit: 0ff93b0e537c4717111a833aeb6d33e63b41d2f6 https://github.com/galaxyproject/galaxy/commit/0ff93b0e537c4717111a833aeb6d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/70128b5d69c0...0ff93b0e537c

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[galaxyproject/galaxy] 1b13bf: Log the pid of the first uWSGI process
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 1b13bfa48e1b3e805a46feec55a3c698ce1fa524 https://github.com/galaxyproject/galaxy/commit/1b13bfa48e1b3e805a46feec55a3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Log the pid of the first uWSGI process So it is the same that gets written to file when using the `--pidfile` option of `uwsgi`. Commit: c6ae97edaef3a146955731aefe510887f4c8b6d0 https://github.com/galaxyproject/galaxy/commit/c6ae97edaef3a146955731aefe51… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Merge pull request #5774 from nsoranzo/release_18.01_fix_pid [18.01] Log the pid of the first uWSGI process Compare: https://github.com/galaxyproject/galaxy/compare/d6be56256fcb...c6ae97edaef3

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[galaxyproject/galaxy] 528201: Add delayed column attribute to grid helper
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 528201e56ac651087fba38d20803ecce320050aa https://github.com/galaxyproject/galaxy/commit/528201e56ac651087fba38d20803… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Add delayed column attribute to grid helper Commit: db1b8bc64b35265faa04268ad382c86067a214bc https://github.com/galaxyproject/galaxy/commit/db1b8bc64b35265faa04268ad382… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Use delayed flag for history grid Commit: 70128b5d69c0c7aef8c6cdfdbd2f84cbeac4f8f5 https://github.com/galaxyproject/galaxy/commit/70128b5d69c0c7aef8c6cdfdbd2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5789 from guerler/add_delay_handler Add delay attribute to grid handler Compare: https://github.com/galaxyproject/galaxy/compare/16291826d2b1...70128b5d69c0

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[galaxyproject/galaxy] 4ae322: Fix history link to visualizations view
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4ae3222e10d6367c2d43b60e138fe9298903b2f3 https://github.com/galaxyproject/galaxy/commit/4ae3222e10d6367c2d43b60e138f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Fix history link to visualizations view Commit: 16291826d2b1852a0823c259d2ce4dcf086b936a https://github.com/galaxyproject/galaxy/commit/16291826d2b1852a0823c259d2ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #5799 from guerler/fix_viz_list Fix history link to visualizations view Compare: https://github.com/galaxyproject/galaxy/compare/fa69c7507ba6...16291826d2b1

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[galaxyproject/galaxy] b4a30b: Revise uwsgi defaults and display.
by GitHub 28 Mar '18

28 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4a30bcd824f5bbb6e68717b508dd522ab640f26 https://github.com/galaxyproject/galaxy/commit/b4a30bcd824f5bbb6e68717b508d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Revise uwsgi defaults and display. In https://github.com/galaxyproject/galaxy/issues/1530 we realized that buffer-size needs to be increased for Galaxy requests. Also mention thunder-lock since that should frequently be enabled - https://github.com/galaxyproject/ansible-galaxy-extras/pull/195. Commit: fa69c7507ba623a378aac517b11087d843f07067 https://github.com/galaxyproject/galaxy/commit/fa69c7507ba623a378aac517b110… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Merge pull request #5743 from jmchilton/uwsg-buffer-size Revise uwsgi defaults and display. Compare: https://github.com/galaxyproject/galaxy/compare/449e25200b20...fa69c7507ba6

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[galaxyproject/galaxy] 04a901: [18.01] Fix SQL query for "workflows shared with m...
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 04a901771b59d1fcf8070cd4c4de1f464e304e55 https://github.com/galaxyproject/galaxy/commit/04a901771b59d1fcf8070cd4c4de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- [18.01] Fix SQL query for "workflows shared with me" as part of workflow index. Before and after queries here: https://gist.github.com/jmchilton/dc57bca60178341d9ce0f6cf6d4bd36f You can see that before the joined load of the stored workflow wasn't being registered by SQLalchemy properly and so it was joining that table twice - once using the proper index and another time just walking the whole table. The filter and order by were being applied to the unconditional version - kind of like saying give me all the workflows and the right workflows and I will check all the workflows to see if this one is deleted instead of just the subset of workflows that are actually being shared with the target user. Commit: d6be56256fcbee53509dc867d863819621ef1d08 https://github.com/galaxyproject/galaxy/commit/d6be56256fcbee53509dc867d863… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #5782 from jmchilton/fix_1801 [18.01] Fix SQL query for "workflows shared with me" as part of workflow index. Commit: 449e25200b2099ddbd253ee7f528ee69e997c2aa https://github.com/galaxyproject/galaxy/commit/449e25200b2099ddbd253ee7f528… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2558d2780109...449e25200b20

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[galaxyproject/galaxy] 04a901: [18.01] Fix SQL query for "workflows shared with m...
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 04a901771b59d1fcf8070cd4c4de1f464e304e55 https://github.com/galaxyproject/galaxy/commit/04a901771b59d1fcf8070cd4c4de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- [18.01] Fix SQL query for "workflows shared with me" as part of workflow index. Before and after queries here: https://gist.github.com/jmchilton/dc57bca60178341d9ce0f6cf6d4bd36f You can see that before the joined load of the stored workflow wasn't being registered by SQLalchemy properly and so it was joining that table twice - once using the proper index and another time just walking the whole table. The filter and order by were being applied to the unconditional version - kind of like saying give me all the workflows and the right workflows and I will check all the workflows to see if this one is deleted instead of just the subset of workflows that are actually being shared with the target user. Commit: d6be56256fcbee53509dc867d863819621ef1d08 https://github.com/galaxyproject/galaxy/commit/d6be56256fcbee53509dc867d863… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #5782 from jmchilton/fix_1801 [18.01] Fix SQL query for "workflows shared with me" as part of workflow index. Compare: https://github.com/galaxyproject/galaxy/compare/fbb47f6e03d0...d6be56256fcb

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[galaxyproject/galaxy] a4e9fe: Merge pull request #1 from galaxyproject/dev
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a4e9fe6834c507137988a1739a3b6a261598ce37 https://github.com/galaxyproject/galaxy/commit/a4e9fe6834c507137988a1739a3b… Author: Delphine Lariviere <lariviere.delphine(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: A .ci/autopep8.sh A .ci/check_py3_compatibility.sh M .ci/first_startup.sh M .ci/flake8_blacklist.txt R .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh R .ci/flake8_wrapper_imports.sh M .ci/jenkins/api/run_tests.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A SECURITY_POLICY.md A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js A client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/Message.vue A 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config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako A config/plugins/visualizations/venn/config/venn.xml A config/plugins/visualizations/venn/package.json A config/plugins/visualizations/venn/src/script.js A config/plugins/visualizations/venn/src/venn.js A config/plugins/visualizations/venn/static/logo.png A config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml A config/plugins/webhooks/demo/tour_generator/script.js A config/plugins/webhooks/demo/tour_generator/styles.css R config/reports.ini.sample A config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A config/user_preferences_extra_conf.yml.sample A config/workflow_resource_mapper_conf.yml.sample A 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test/manual/workflows_scaling.py R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-qunit-1.0.0.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js R test/qunit/tests/job-dag.html R test/qunit/tests/job-dag.js R test/qunit/tests/list-of-pairs-collection-creator.html R test/qunit/tests/list-of-pairs-collection-creator.js R test/qunit/tests/masthead_tests.html R test/qunit/tests/masthead_tests.js R test/qunit/tests/metrics-logger.html R test/qunit/tests/metrics-logger.js R test/qunit/tests/modal_tests.html R test/qunit/tests/modal_tests.js R test/qunit/tests/page_tests.html R test/qunit/tests/page_tests.js R test/qunit/tests/popover_tests.html R test/qunit/tests/popover_tests.js R test/qunit/tests/ui_tests.html R test/qunit/tests/ui_tests.js R test/qunit/tests/upload_dialog_tests.html R test/qunit/tests/upload_dialog_tests.js R test/qunit/tests/utils_test.html R test/qunit/tests/utils_test.js R test/qunit/tests/workflow_editor_tests.html R test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1 from galaxyproject/dev Update from Galaxyproject repo Commit: ed86fe745f53b151dce03cf571f306d293e59ab9 https://github.com/galaxyproject/galaxy/commit/ed86fe745f53b151dce03cf571f3… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/gbkgz_to_genbank.xml A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/sequence.py Log Message: ----------- add genbank.gz andgbk.gz datatypes Commit: 1e7c86323258676938a060077fca8ad8a41d43e4 https://github.com/galaxyproject/galaxy/commit/1e7c86323258676938a060077fca… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- addition of blank lines (test failures) Commit: e0b9e93b4b76e4e9d553e61f2faa71d6bf559981 https://github.com/galaxyproject/galaxy/commit/e0b9e93b4b76e4e9d553e61f2faa… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/converters/gbkgz_to_genbank.xml M lib/galaxy/datatypes/sequence.py Log Message: ----------- removed gbk.gz extension Commit: a97b3a469c83f8f6780fd0b84f70ea31e08b6f91 https://github.com/galaxyproject/galaxy/commit/a97b3a469c83f8f6780fd0b84f70… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M tox.ini Log Message: ----------- fex sniffing of compressed genbank files also add doctest for both compressed and uncompressed versions Commit: 2558d278010999b96aaf279c4eaf539614844de7 https://github.com/galaxyproject/galaxy/commit/2558d278010999b96aaf279c4eaf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/sequence.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M tox.ini Log Message: ----------- Merge pull request #5772 from Delphine-L/addGbkgz Add genbank.gz datatype Compare: https://github.com/galaxyproject/galaxy/compare/c5beedef6b9f...2558d2780109

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[galaxyproject/galaxy] 571fed: Remove menu options from visualization tab, shift ...
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 571fedf00654c36ee60115abff50d4d4d4031a5b https://github.com/galaxyproject/galaxy/commit/571fedf00654c36ee60115abff50… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/buildapp.py M static/style/blue/base.css Log Message: ----------- Remove menu options from visualization tab, shift tab to workflows Commit: 0bd98c320ee0ca8c998dfbfc8f84a174066969a7 https://github.com/galaxyproject/galaxy/commit/0bd98c320ee0ca8c998dfbfc8f84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: A lib/galaxy/webapps/galaxy/api/plugins.py Log Message: ----------- Add plugins endpoint Commit: cc3e5244d603e13afcf4501aefc88868e971fe50 https://github.com/galaxyproject/galaxy/commit/cc3e5244d603e13afcf4501aefc8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/plugins.py Log Message: ----------- Remove unused imports from plugins api endpoint Commit: 1ca6499ea10c35d1647898d50dfac442055fa1cc https://github.com/galaxyproject/galaxy/commit/1ca6499ea10c35d1647898d50dfa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/PluginList.vue M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add vue list for plugins Commit: f4e52caab6027a50b631331ad3cd02fd3ca2a0a8 https://github.com/galaxyproject/galaxy/commit/f4e52caab6027a50b631331ad3cd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Remove id from header value Commit: 82e58d9086e7e0da86aab270d07bf8ff442cb2e4 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lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Remove comment and debug output Commit: 15636fa6f144f4a2203b76df0b47cd7d70d03ada https://github.com/galaxyproject/galaxy/commit/15636fa6f144f4a2203b76df0b47… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Revise resource mapping, add show action to plugins endpoint Commit: a8daf446eab87cffb5483a6d96b5f8d244d8286c https://github.com/galaxyproject/galaxy/commit/a8daf446eab87cffb5483a6d96b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M lib/galaxy/webapps/galaxy/api/plugins.py Log Message: ----------- Add error handlers, populate select list with applicable datasets Commit: b6ad62c0e09d3c67951849cdaeb340e9bc9f11a0 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923286612d7e31ffaf474a60392960f36345895f https://github.com/galaxyproject/galaxy/commit/923286612d7e31ffaf474a603929… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Revise dataset selection label Commit: a077f45ba9830136f2869e39e50680e7dfc41c5b https://github.com/galaxyproject/galaxy/commit/a077f45ba9830136f2869e39e506… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Match search word with description Commit: 980f2b9708cb9e95bbacf0ae0decb42f7cd0da6c https://github.com/galaxyproject/galaxy/commit/980f2b9708cb9e95bbacf0ae0dec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js Log Message: ----------- Partial fix for internal scatterplot Commit: a6559248c9e877911ed86b08135f7aae6408fb0b https://github.com/galaxyproject/galaxy/commit/a6559248c9e877911ed86b08135f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M config/plugins/visualizations/scatterplot/src/scatterplot.js Log Message: ----------- Remove comments Commit: 044ca897d53c08939508935c003c5e3d665ba769 https://github.com/galaxyproject/galaxy/commit/044ca897d53c08939508935c003c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml Log Message: ----------- Add confirm option Commit: 58f0afe23b9c9590bd8cda1dd4d7c3b731fb0969 https://github.com/galaxyproject/galaxy/commit/58f0afe23b9c9590bd8cda1dd4d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Hide grid if error occurs Commit: eec8bf47036c0057f9a21578159199b6c036acbb https://github.com/galaxyproject/galaxy/commit/eec8bf47036c0057f9a215781591… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Augment button model with visibile attribute Commit: 7f342c340e7739854a1cd7fda375d947aa8addb2 https://github.com/galaxyproject/galaxy/commit/7f342c340e7739854a1cd7fda375… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Fix default inline handler, fix fullscreen switch Commit: 4f4c8967c0de717f27b5057aaeaef8e3b4d0da98 https://github.com/galaxyproject/galaxy/commit/4f4c8967c0de717f27b5057aaeae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml Log Message: ----------- Fix modified handler Commit: f47b88730b2dba31daeeba76f76b06aea44fdbc6 https://github.com/galaxyproject/galaxy/commit/f47b88730b2dba31daeeba76f76b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js Log Message: ----------- Remove unused variable Commit: bebc022d6f6c6a0dff627381c7c435fffbdbe3e0 https://github.com/galaxyproject/galaxy/commit/bebc022d6f6c6a0dff627381c7c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Add info notification for visualizations which require additional confirmation Commit: 5e98958c22dba2665f762052e4d017145a243395 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lib/galaxy/util/monitors.py M lib/galaxy/util/none_like.py M lib/galaxy/util/path/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/scheduling_manager.py M scripts/migrate_tools/migrate_tools.py R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako A test-data/qname_sorted.bam M test/functional/tools/multi_output_recurse.xml M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/unit/tools/test_toolbox.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: 04bfefb7dae2a0d035d76f57a6c552facee8bd19 https://github.com/galaxyproject/galaxy/commit/04bfefb7dae2a0d035d76f57a6c5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/galaxy.yml.sample M config/plugins/webhooks/demo/tour_generator/__init__.py M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/util/workflow_util.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M static/style/blue/base.css M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: e57136523c5e5674c1091cfcec601a5b65fc3fd3 https://github.com/galaxyproject/galaxy/commit/e57136523c5e5674c1091cfcec60… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Fix trackster urls Commit: 840ad914c5a3ce7ad7b8fd2f4c4f5bf051543c95 https://github.com/galaxyproject/galaxy/commit/840ad914c5a3ce7ad7b8fd2f4c4f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Move url creation to plugins Commit: f3eb82208971e151399ac2c7d7539d7d8ca1630b https://github.com/galaxyproject/galaxy/commit/f3eb82208971e151399ac2c7d753… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Revise url generator Commit: 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config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png Log Message: ----------- Add description for trackster and other visualizations Commit: dc3cd003549cd9f54e7a955af8e7ecec355c2a44 https://github.com/galaxyproject/galaxy/commit/dc3cd003549cd9f54e7a955af8e7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/unipept/config/unipept.xml Log Message: ----------- Add additional descriptions Commit: ace94178c8af8cbd8d098229d96a7a27104da798 https://github.com/galaxyproject/galaxy/commit/ace94178c8af8cbd8d098229d96a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- Revise data submission tool Commit: 553474ddfd32229787630989099127e8029dd4f9 https://github.com/galaxyproject/galaxy/commit/553474ddfd322297876309890991… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/example/config/example.xml Log Message: ----------- Hide example plugin Commit: f08223bc7a7ac7e9827543601707009c2ac8a0f1 https://github.com/galaxyproject/galaxy/commit/f08223bc7a7ac7e9827543601707… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Sort plugins by display name Commit: 7d95d28d7c729ff25fe8f9f21e9bd7fcad183cbe https://github.com/galaxyproject/galaxy/commit/7d95d28d7c729ff25fe8f9f21e9b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/trackster/config/trackster.xml Log Message: ----------- Increase priority for trackster Commit: e0c25f42668f3956ee152843057fda74cdea79a4 https://github.com/galaxyproject/galaxy/commit/e0c25f42668f3956ee152843057f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/plugins/visualizations/example/config/example.xml Log Message: ----------- Enable example Commit: 1aa5f8283eaaf5f03b929215ffd49982a74febc2 https://github.com/galaxyproject/galaxy/commit/1aa5f8283eaaf5f03b929215ffd4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Fix lint Commit: 7afecf9d1ab0b5d6ad5c34a180ff599b318bc0a1 https://github.com/galaxyproject/galaxy/commit/7afecf9d1ab0b5d6ad5c34a180ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Fix test cases Commit: 00f282ccaab220d290a298f28fe8d9b113cf908b https://github.com/galaxyproject/galaxy/commit/00f282ccaab220d290a298f28fe8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Use vue instead of backbone view Commit: cb9ecb63f533dfc648af1b016975f89cb2591bfe https://github.com/galaxyproject/galaxy/commit/cb9ecb63f533dfc648af1b016975… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: R client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Remove backbone visualization selector Commit: b325e086f20f241bc2c2a39a705b7d12bda5e06d https://github.com/galaxyproject/galaxy/commit/b325e086f20f241bc2c2a39a705b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Remove unused import Commit: 9f52c391229d07687dfa792fa525cb8c781e3b93 https://github.com/galaxyproject/galaxy/commit/9f52c391229d07687dfa792fa525… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Use parsed dataset id in visualization selector instead of showing select field Commit: 21aa7462875f064766be2e5a6e7b35f7de7dc2b0 https://github.com/galaxyproject/galaxy/commit/21aa7462875f064766be2e5a6e7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Fix button inline style Commit: c14ed8732f76cab4e72371878fd770fc01c7bfb0 https://github.com/galaxyproject/galaxy/commit/c14ed8732f76cab4e72371878fd7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Temporary use of style section in vue component Commit: 9bb1e48aba4bd5de3d0b59b113d8dce2d047612b https://github.com/galaxyproject/galaxy/commit/9bb1e48aba4bd5de3d0b59b113d8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/job_metrics_conf.xml.sample M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py A lib/galaxy/jobs/metrics/instrumenters/cgroup.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/special_tools.py M lib/galaxy/util/compression_utils.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A test-data/1.csv A test-data/example-bag.zip A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into visualization_header Commit: a706929bd6fe7f9d502e756cc592806a79480147 https://github.com/galaxyproject/galaxy/commit/a706929bd6fe7f9d502e756cc592… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M config/datatypes_conf.xml.sample A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M lib/galaxy/containers/docker_model.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml R lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/script.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/util/tool_util.py M test/functional/test_toolbox.py R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: ef619f5905820d635f068a5c372b4167dec121bd https://github.com/galaxyproject/galaxy/commit/ef619f5905820d635f068a5c372b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M doc/source/releases/18.01_announce.rst M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/run_request.py M scripts/common_startup.sh M test/api/test_workflows.py Log Message: ----------- Merge branch 'dev' into visualization_header Commit: c07c17e93dbd137947320b417082733a8a34345e https://github.com/galaxyproject/galaxy/commit/c07c17e93dbd137947320b417082… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M config/plugins/visualizations/msa/static/script.js Log Message: ----------- Restore missing 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client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/decorators.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/root.py M test/base/driver_util.py Log Message: ----------- Merge branch 'dev' into visualization_header Commit: df5838e6c1924e2f0303c675e0262736ece52238 https://github.com/galaxyproject/galaxy/commit/df5838e6c1924e2f0303c675e026… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed 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client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M 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lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M run_tests.sh A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into visualization_header Commit: 8b5c0b223ef9092420b9912b153b0d257fe5a1a5 https://github.com/galaxyproject/galaxy/commit/8b5c0b223ef9092420b9912b153b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue Log Message: ----------- Allow target top rendering for visualizations Commit: 0cdd9b9ecd235a34ba6018542156f9780bf22f77 https://github.com/galaxyproject/galaxy/commit/0cdd9b9ecd235a34ba6018542156… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Client formatting Commit: 2b2fd9289857b258f7e63f64668d776c49a54ec8 https://github.com/galaxyproject/galaxy/commit/2b2fd9289857b258f7e63f64668d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Use visualizations route to link to plugins Commit: 38c2a895009c03204026ca7d74af70f92dd29f4e https://github.com/galaxyproject/galaxy/commit/38c2a895009c03204026ca7d74af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge branch 'visualization_header' of github.com:guerler/galaxy into visualization_header Commit: c5beedef6b9f4498e4df0adfb39ddc519715f997 https://github.com/galaxyproject/galaxy/commit/c5beedef6b9f4498e4df0adfb39d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/charts.less M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/buildapp.py M static/style/blue/base.css M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge branch 'visualization_header' into dev Compare: https://github.com/galaxyproject/galaxy/compare/bf5d472e2850...c5beedef6b9f

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[galaxyproject/usegalaxy-playbook] 6f9370: Upgraded dunovo on test and main, upgraded extract...
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f9370135835b80ee1a1ec77d0133ae4aec364bf https://github.com/galaxyproject/usegalaxy-playbook/commit/6f9370135835b80e… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Upgraded dunovo on test and main, upgraded extract genomic dna on main.

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[galaxyproject/galaxy] db47c8: Remove prepopulation of column selector
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: db47c876ee69bd034b7e131daf0a7fd5672d2221 https://github.com/galaxyproject/galaxy/commit/db47c876ee69bd034b7e131daf0a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove prepopulation of column selector Commit: fc7beca6d1d379ddfc1ea4769edfc8c22d74fb10 https://github.com/galaxyproject/galaxy/commit/fc7beca6d1d379ddfc1ea4769edf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Create input element combining text and select options Commit: 2e8c9489bfd149d12b9498ea89c5633a07509d48 https://github.com/galaxyproject/galaxy/commit/2e8c9489bfd149d12b9498ea89c5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix value handling, remove redundant value check Commit: 9fbdcd1d5ee84887c28eed727fec77d402ef95fa https://github.com/galaxyproject/galaxy/commit/9fbdcd1d5ee84887c28eed727fec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Relax validation conditions Commit: ff874dc4e4f4d21bb133b2730058393c7ae7a66a https://github.com/galaxyproject/galaxy/commit/ff874dc4e4f4d21bb133b2730058… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Properly switch between states, transfer current value Commit: 9fff4f1615aa7ce02561d681ae20397b22b17f02 https://github.com/galaxyproject/galaxy/commit/9fff4f1615aa7ce02561d681ae20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove redundant initial value checks, value can only be empty Commit: 1db1c0c77122edd183ab6f0bf5da24c94c83b476 https://github.com/galaxyproject/galaxy/commit/1db1c0c77122edd183ab6f0bf5da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Revise condition, check explicitly for none Commit: 608f3dc9d3ed59a21fba221f590240ecfdc1294a https://github.com/galaxyproject/galaxy/commit/608f3dc9d3ed59a21fba221f5902… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add check for column index values Commit: f4f275f82aa9b1e19aafe0525b4006876905ef96 https://github.com/galaxyproject/galaxy/commit/f4f275f82aa9b1e19aafe0525b40… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add dataset state check to column input Commit: a144eb1fb40eee0920e8153b3e51304c10130003 https://github.com/galaxyproject/galaxy/commit/a144eb1fb40eee0920e8153b3e51… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix integer test Commit: 29337d2b7b1d51c44ff621049483037fd9d48d1a https://github.com/galaxyproject/galaxy/commit/29337d2b7b1d51c44ff621049483… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Simplify legal value length check Commit: 05ce42d229db08c6af7425f1afe1eea625dfd1da https://github.com/galaxyproject/galaxy/commit/05ce42d229db08c6af7425f1afe1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Provide value for column index if not an integer Commit: 9febc519944dcfb5c8907b8a302fd6aff6f0f79f https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Identify implicit conversions, check reference context for datasets Commit: 1baafd07ffbaa42bd5071a659ccb82203591afa0 https://github.com/galaxyproject/galaxy/commit/1baafd07ffbaa42bd5071a659ccb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Move implicit dataset tagging to dataset state check Check attribute Commit: dae6cc7f4cb403cdee44c532f314f639d8e9f96b https://github.com/galaxyproject/galaxy/commit/dae6cc7f4cb403cdee44c532f314… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indent Commit: f305c0b0ab9182af0578078c622d024a57b9b05d https://github.com/galaxyproject/galaxy/commit/f305c0b0ab9182af0578078c622d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Reinsert legal value check handler Commit: c7e794745b1b7699a7ac34caaa684f298f562dbc https://github.com/galaxyproject/galaxy/commit/c7e794745b1b7699a7ac34caaa68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Validate value before matching dataset Commit: 81a418fe98ee2f26b35bae81060398431b9a096e https://github.com/galaxyproject/galaxy/commit/81a418fe98ee2f26b35bae810603… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove explicit integer validation Commit: 187c540cd4aac7e1059fdaa6aaf56c87913f1d09 https://github.com/galaxyproject/galaxy/commit/187c540cd4aac7e1059fdaa6aaf5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix test case Commit: 04fee6070bfa94a3788c89dc0cc1414469db20e6 https://github.com/galaxyproject/galaxy/commit/04fee6070bfa94a3788c89dc0cc1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into select_to_text Commit: ade62bc3b15b25e76d7114c5ee9051cd5f575700 https://github.com/galaxyproject/galaxy/commit/ade62bc3b15b25e76d7114c5ee90… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Revise select display matching Commit: 8290da24eaf0994c018b055ba9bbc73876540f7c https://github.com/galaxyproject/galaxy/commit/8290da24eaf0994c018b055ba9bb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indentation Commit: 241ade62cd740bf62d2348859493ed7326799597 https://github.com/galaxyproject/galaxy/commit/241ade62cd740bf62d2348859493… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Align validation order for consistency Commit: 2b3557ffce38a97080c9921846e06131aa43e2e9 https://github.com/galaxyproject/galaxy/commit/2b3557ffce38a97080c9921846e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix test case verifying we check column values before tool execution. Commit: 91e97b60968d6813bd7a28d0d60e778b288ac385 https://github.com/galaxyproject/galaxy/commit/91e97b60968d6813bd7a28d0d60e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Refactor code for clarity Commit: 840e436ea1f181ebe0c8478145e2cd0e97dc1778 https://github.com/galaxyproject/galaxy/commit/840e436ea1f181ebe0c8478145e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add strict workflow building mode check to drill downs Commit: bf5d472e28505438c5f345ad29989b80fe3aae80 https://github.com/galaxyproject/galaxy/commit/bf5d472e28505438c5f345ad2998… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5702 from guerler/select_to_text Relax validation condition for dynamic parameters Compare: https://github.com/galaxyproject/galaxy/compare/61adffbd614c...bf5d472e2850

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[galaxyproject/galaxy] 527412: Use pipenv also for the default dependencies
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 52741200b24933d3c4af1f5a7fa5124d29d5daf6 https://github.com/galaxyproject/galaxy/commit/52741200b24933d3c4af1f5a7fa5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Use pipenv also for the default dependencies Commit: fb92257bc755ae12a5dad810c152967bfc68d8a1 https://github.com/galaxyproject/galaxy/commit/fb92257bc755ae12a5dad810c152… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Exclude 2 problematic h5py versions A warning was appearing in the stderr of upload jobs due to https://github.com/h5py/h5py/issues/995 . Commit: f8aa29e2805b932a03a577fd329f881a3d047c98 https://github.com/galaxyproject/galaxy/commit/f8aa29e2805b932a03a577fd329f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Temporarily pin WebOb to latest compatible release Commit: e625b649dc0e823d0c92f8c997254215bcf9dcab https://github.com/galaxyproject/galaxy/commit/e625b649dc0e823d0c92f8c99725… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Temporarily pin Mercurial to latest compatible release Commit: 61adffbd614cbbe409f207415073604f8e13a0ba https://github.com/galaxyproject/galaxy/commit/61adffbd614cbbe409f207415073… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5786 from nsoranzo/default_pipfile Use pipenv also for the default dependencies Compare: https://github.com/galaxyproject/galaxy/compare/5a86b8d706b7...61adffbd614c

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[galaxyproject/usegalaxy-playbook] d30a0a: Installed SnpEff version 4.3.1t on test and main.
by GitHub 27 Mar '18

27 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d30a0a9f96d63ec2d9c83cd05b67fdcc56177bfa https://github.com/galaxyproject/usegalaxy-playbook/commit/d30a0a9f96d63ec2… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed SnpEff version 4.3.1t on test and main.

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