galaxy-commits March 2018

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[galaxyproject/galaxy] 03287e: Bugfix in upload_common -- ensure hda is added to ...
by GitHub 31 Mar '18

31 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03287ed195d65ce305e6414ed3659e43c9ac8444 https://github.com/galaxyproject/galaxy/commit/03287ed195d65ce305e6414ed365… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Bugfix in upload_common -- ensure hda is added to a session prior to state setting. Commit: a8072a1d8bf2bf5e232649df61fc6f954164fca3 https://github.com/galaxyproject/galaxy/commit/a8072a1d8bf2bf5e232649df61fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Merge pull request #5816 from dannon/upload_common_bugfix Bugfix in upload_common -- ensure hda is added to a session Compare: https://github.com/galaxyproject/galaxy/compare/e552bc4cbb59...a8072a1d8bf2

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[galaxyproject/galaxy] 9e71e1: Allow anonymous users to view their jobs via the A...
by GitHub 31 Mar '18

31 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e71e1d2f0e7c6586b3f5946edb033466a495258 https://github.com/galaxyproject/galaxy/commit/9e71e1d2f0e7c6586b3f5946edb0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Allow anonymous users to view their jobs via the API. Commit: 083bdcbdd84da29b1e2692058bbebd6426e8b2ae https://github.com/galaxyproject/galaxy/commit/083bdcbdd84da29b1e2692058bbe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M client/package.json A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Rule-based Collection Builder Vue-based component for defining collections by applying rules to a list of files or more general spreadsheet style information (e.g. sample sheets or tabular data from data sources containing URL or FTP file paths for files along with metadata). The widget is fairly complex but very broadly is broken into two panes - one to preview how rules are applied to build up tabular data defining collections (each row corresponding to a file with columns for metadata and such) and one that displays defined rules and allows for editing of these rules and creation of new ones. The goal behind defining rules this way instead of allowing the user to interact with the spreadsheet display directly is to enable scaling up collection creation. If a user wishes to upload hundreds of datasets - interacting with a widget directly for each input doesn't scale well and would be error prone. If a user wishes to upload hundreds of thousands of datasets - even loading this information in the GUI may not scale (though I've been impressed with the performance so far of this approach) and so we can potentially just display a preview of some of the rows and process the final set of rules on the backend. Since we can handle an arbitrary number of columns this way, we can define multiple list identifiers per file and so we can easily construct nested lists. Hence this allows creation of not just potentially larger collections but arbitrarily complex lists as well. Paired identifiers via indicator columns are also implemented. In order to operate over lists of datasets directly - the multi-select history widget now has a new option "Build Collection from Rules" along side the other collection builders. This mode uses the well established dataset collection API to build collections from HDAs. In order to operate on lists of FTP files or URLs - the upload widget has a new tab "Rule-based" tab that allows users to paste in tabular data or select a history dataset and then send this tabular data to the new builder widget. This will be extended to include FTP directories for instance over time. This mode uses the new data fetch API to build collections and handle uploads of arbitrary collections of files. The preview of the tabular data generated via rules is done via [Handsontable](https://handsontable.com/) - a JavaScript spreadsheet widget with a VueJS [wrapper component](https://github.com/handsontable/vue-handsontable-official). This turns out to be a fairly nice application for reactive components - as rules are added or modified the spreadsheet just naturally updates. In my hands the widget scales very nicely - I've uploaded files with tens of thousands of rows and rules modifying the data and changing the spreadsheet do not seem to cause siignificant delays in the web browser. Commit: ebf08c16493b8fd3e770bf3c33c1f3eea55dd374 https://github.com/galaxyproject/galaxy/commit/ebf08c16493b8fd3e770bf3c33c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/webpack.config.js Log Message: ----------- Fix production build of vue-handsontable Commit: cfa1208a79dcd0bdda5c7632366c2bd2b6deea0d https://github.com/galaxyproject/galaxy/commit/cfa1208a79dcd0bdda5c7632366c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/yarn.lock Log Message: ----------- Yarn lock w/ new deps. Commit: b32e78f338fcbd586f77c64f0fa18aee6ce23d1b https://github.com/galaxyproject/galaxy/commit/b32e78f338fcbd586f77c64f0fa1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix upload view initialization. Commit: 1c04bbe9f6a95c1c8050bc5a8cd69bd8030cf350 https://github.com/galaxyproject/galaxy/commit/1c04bbe9f6a95c1c8050bc5a8cd6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/.babelrc M client/package.json M client/yarn.lock Log Message: ----------- Add babel plugin for vue template preprocessing. This allows precompilation without a vue runtime for nested local components in vue SFCs, and other situations. Commit: e552bc4cbb592eb2fcb4658e287026a742aab286 https://github.com/galaxyproject/galaxy/commit/e552bc4cbb592eb2fcb4658e2870… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/.babelrc A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M client/package.json M client/webpack.config.js M client/yarn.lock M lib/galaxy/webapps/galaxy/api/jobs.py A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #5365 from jmchilton/rule_based_uploader Rule-based Uploader / Builder Compare: https://github.com/galaxyproject/galaxy/compare/ac74b7ffb221...e552bc4cbb59

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[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

1 0

[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

1 0

[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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