galaxy-commits August 2018

galaxy-commits@lists.galaxyproject.org

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72 discussions

[galaxyproject/usegalaxy-playbook] 241e79: Updated plant tribes scaffold downloader.
by GitHub 20 Aug '18

20 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 241e79e5f0570da937b888956aaba8943d3b5ad4 https://github.com/galaxyproject/usegalaxy-playbook/commit/241e79e5f0570da9… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated plant tribes scaffold downloader. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] bf206c: Reorder inputs before multiplications
by GitHub 20 Aug '18

20 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf206c870b793edda71aaa5655baeca070e3729a https://github.com/galaxyproject/galaxy/commit/bf206c870b793edda71aaa5655ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py M lib/galaxy/util/permutations.py Log Message: ----------- Reorder inputs before multiplications This should be a stable order. Ideally this would be configurable to the user or tool auther, but for now this is based on the order within which data paramaters appear in tool.inputs, which depends on the order in the XML/YML. If this isn't stable the order of the input combinations may change, and elements will jump in the collection structure. For instance the reverse:forward output for a pair:pair in inputA multiplied by pair:pair in input B may end up in forward:reverse if re-run. Commit: 9138651bdd92e0eb1fe2ea2b2099b5b2f04f655d https://github.com/galaxyproject/galaxy/commit/9138651bdd92e0eb1fe2ea2b2099… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Serialize JobParamters with sort_keys=True This wasn't a bigger issue on python 2 for the same reason that the input ordering in the previous commit didn't matter. I hope it'll make the test_workflow_rerun_with_use_cached_job test that is marked as flakey stable as well. Commit: 2d60d9af0132c4975ae636d161097140b72e6fbc https://github.com/galaxyproject/galaxy/commit/2d60d9af0132c4975ae636d16109… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Wait for first workflow when testing cache That should make the test less flakey. While in theory we should be able to replace scheduled workflow jobs with cached jobs, this is not what we're testing here, and I assume it doesn't work for now. Commit: 7160b7f4e48e0c611758aea890771fea07a059ec https://github.com/galaxyproject/galaxy/commit/7160b7f4e48e0c611758aea89077… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- No kwargs for rsplit on python 2 Commit: 85f347e1c6597523b0e8718d7a93d4dc27cac2f9 https://github.com/galaxyproject/galaxy/commit/85f347e1c6597523b0e8718d7a93… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/util/permutations.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6609 from mvdbeek/fix_random_implicit_collection_order Order data parameters before unlinked multiplication Compare: https://github.com/galaxyproject/galaxy/compare/f5bd245faaaa...85f347e1c659 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 283947: Update ucsc genome-test server URL.
by GitHub 17 Aug '18

17 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2839475967320b7d95ade125e542625c6d54c1b9 https://github.com/galaxyproject/galaxy/commit/2839475967320b7d95ade125e542… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Update ucsc genome-test server URL. Commit: 1cd36e3f815b6ad06da7a1aa1ee2c56d67edc36c https://github.com/galaxyproject/galaxy/commit/1cd36e3f815b6ad06da7a1aa1ee2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Bump version; 'patch' since it should be the exact same, as much as anything over the net ever could be\? Commit: 6cbb574553a882b7573d86f25bede17e7293cc76 https://github.com/galaxyproject/galaxy/commit/6cbb574553a882b7573d86f25bed… Author: Matthew Spelchak <mrs11teen(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- Fix Location of Plugin Static Content Commit: 7e445be502a64213c96cb233200aa0f53a2821f4 https://github.com/galaxyproject/galaxy/commit/7e445be502a64213c96cb233200a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- Merge pull request #6602 from phac-nml/ie_documentation_fix [18.05] Fix Location of Plugin Static Content In Documentation for 18.05 Commit: 709e49f104e2cba5d180bffb0ed0fee175f5ffba https://github.com/galaxyproject/galaxy/commit/709e49f104e2cba5d180bffb0ed0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Merge pull request #6591 from dannon/ucsc-test-server-domain [18.05] Update UCSC genome-test server URLs Commit: f5bd245faaaa90693d8a5739f60bc863f545762f https://github.com/galaxyproject/galaxy/commit/f5bd245faaaa90693d8a5739f60b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M doc/source/admin/special_topics/interactive_environments.rst M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2c6900930c24...f5bd245faaaa **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] dac763: Keep unicode tags
by GitHub 17 Aug '18

17 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dac763a665703e84bd7cd29f63de60dd75fd305c https://github.com/galaxyproject/galaxy/commit/dac763a665703e84bd7cd29f63de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Keep unicode tags Should fix ``` selenium.webdriver.remote.remote_connection DEBUG 2018-08-16 19:17:13,852 Finished Request galaxy.web.framework.decorators ERROR 2018-08-16 19:17:13,858 Uncaught exception in exposed API method: Traceback (most recent call last): File "/galaxy/lib/galaxy/web/framework/decorators.py", line 157, in decorator rval = func(self, trans, *args, **kwargs) File "/galaxy/lib/galaxy/web/framework/decorators.py", line 77, in decorator return func(self, trans, *args, **kwargs) File "/galaxy/lib/galaxy/webapps/galaxy/controllers/history.py", line 317, in list return self.stored_list_grid(trans, **kwargs) File "/galaxy/lib/galaxy/web/framework/helpers/grids.py", line 139, in __call__ query = column.filter(trans, trans.user, query, column_filter) File "/galaxy/lib/galaxy/web/framework/helpers/grids.py", line 664, in filter query = query.filter(self.get_filter(trans, user, column_filter)) File "/galaxy/lib/galaxy/web/framework/helpers/grids.py", line 703, in get_filter raw_tags = trans.app.tag_handler.parse_tags(column_filter.encode("utf-8")) File "/galaxy/lib/galaxy/managers/tags.py", line 260, in parse_tags raw_tags = reg_exp.split(tag_str) TypeError: cannot use a string pattern on a bytes-like object ``` Commit: 85f76945777b09958488672ef1a7c456d2bc5980 https://github.com/galaxyproject/galaxy/commit/85f76945777b09958488672ef1a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Fix one more case of tag encoding Commit: 2c6900930c2454979fcc96e9159bdbbe44bafc3b https://github.com/galaxyproject/galaxy/commit/2c6900930c2454979fcc96e9159b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Merge pull request #6610 from mvdbeek/fix_selenium_py3_tests Fix remaining selenium py3 test failures Compare: https://github.com/galaxyproject/galaxy/compare/d9f394793897...2c6900930c24 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 868a32: Downtime banner
by GitHub 16 Aug '18

16 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 868a321bc326741adaafb1e8e2e08176d56078bf https://github.com/galaxyproject/usegalaxy-playbook/commit/868a321bc326741a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Downtime banner **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 562432: Add framework_py3 test target
by GitHub 16 Aug '18

16 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5624323a337a5d6176d3bb9be3bef599e65167b1 https://github.com/galaxyproject/galaxy/commit/5624323a337a5d6176d3bb9be3be… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: A .ci/jenkins/framework-py3/run_tests.sh M run_tests.sh Log Message: ----------- Add framework_py3 test target Commit: fc464f975878867ddc8ef90818db9faab31c7368 https://github.com/galaxyproject/galaxy/commit/fc464f975878867ddc8ef90818db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M test/functional/tools/metadata_biom1.xml Log Message: ----------- Allow 4 lines diff to acount for the prefix of python2 unicode strings Commit: 58067b4c896df7f2f48f3c7b6f4c92f9c6d6f265 https://github.com/galaxyproject/galaxy/commit/58067b4c896df7f2f48f3c7b6f4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix count_lines function for compressed datatypes that inherit from Text Commit: 79ec064214030badbc64694213db0ce4865b5e64 https://github.com/galaxyproject/galaxy/commit/79ec064214030badbc64694213db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- py3: Fix Biom1 datatype Commit: 37132212fe5e1fdf7f43e41c59eac051bfb8f389 https://github.com/galaxyproject/galaxy/commit/37132212fe5e1fdf7f43e41c59ea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/jobs/splitters/multi.py Log Message: ----------- py3: Fix file splitting for parallelism Commit: f831c616cb418f72baa1aae420b47a49a0aacc3c https://github.com/galaxyproject/galaxy/commit/f831c616cb418f72baa1aae420b4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- py3: fix paths_as_file functionality Commit: 70640071224745f61d756ed1475b5a03c85f4f40 https://github.com/galaxyproject/galaxy/commit/70640071224745f61d756ed1475b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Don't log error to provide arguments to __new__ for types that don't take arguments This is just very verbose and unneeded. Commit: ea0e3ffeb779fee900aa8dbc33773a921e39ec9c https://github.com/galaxyproject/galaxy/commit/ea0e3ffeb779fee900aa8dbc3377… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- py3: Fix dataset dataset collection Commit: a927413df22ff3454cf6c691f851cf54673eefb7 https://github.com/galaxyproject/galaxy/commit/a927413df22ff3454cf6c691f851… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M test/functional/tools/parallelism.xml M test/functional/tools/parallelism_optional.xml Log Message: ----------- Use exit code and quote file parameters for paralellism test tools Commit: b041e41155ac18252c46364ac409a9695d9f8bfb https://github.com/galaxyproject/galaxy/commit/b041e41155ac18252c46364ac409… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Write configfile in binary mode This fixes the unicode_stream tool on docker. Commit: 79decc3ba77c5fbcaf36a0cbb9aace16512bcf9d https://github.com/galaxyproject/galaxy/commit/79decc3ba77c5fbcaf36a0cbb9aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Use OrderedDict to collect implicit collections This should fix randomly failing tests that rely on the order of the implcit collection elements, like `test_map_over_two_collections_unlinked`. Commit: c430d4a6509375c5aaf658f149b3038aa8f34883 https://github.com/galaxyproject/galaxy/commit/c430d4a6509375c5aaf658f149b3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Fix selenium test setup Commit: 3957ed91e2d25faae9100c85bc19b9a1c5b3d68e https://github.com/galaxyproject/galaxy/commit/3957ed91e2d25faae9100c85bc19… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M templates/display_common.mako M templates/legacy/grid_base.mako M templates/tagging_common.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Fix errors found during selenium testing Commit: ae9effa61005504c51ca11adbbf6b70f95fab3b8 https://github.com/galaxyproject/galaxy/commit/ae9effa61005504c51ca11adbbf6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: A .ci/jenkins/selenium-py3/run_tests.sh Log Message: ----------- Add selenium py3 jenkins setup Commit: fb86e96bffecaef3861ce68db963c22aee193d54 https://github.com/galaxyproject/galaxy/commit/fb86e96bffecaef3861ce68db963… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Skip decoding to unicode strings in grids At this point we should not have bytestrings anymore (we might, but if we do we should fix that instead). Commit: 7559b90a692a72da2556c61b65c8615ddff822a5 https://github.com/galaxyproject/galaxy/commit/7559b90a692a72da2556c61b65c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/base/driver_util.py M test/functional/test_toolbox.py A test/functional/test_toolbox_pytest.py Log Message: ----------- Setup a simple pytest tool test Commit: d9f394793897a4429664027cbdaacbb8fca6d4e2 https://github.com/galaxyproject/galaxy/commit/d9f394793897a4429664027cbdaa… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: A .ci/jenkins/framework-py3/run_tests.sh A .ci/jenkins/selenium-py3/run_tests.sh M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/web/framework/helpers/grids.py M run_tests.sh M templates/display_common.mako M templates/legacy/grid_base.mako M templates/tagging_common.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/base/driver_util.py M test/functional/test_toolbox.py A test/functional/test_toolbox_pytest.py M test/functional/tools/metadata_biom1.xml M test/functional/tools/parallelism.xml M test/functional/tools/parallelism_optional.xml Log Message: ----------- Merge pull request #6605 from mvdbeek/enable_and_fix_framework_py3_test Enable and fix framework py3 tests Compare: https://github.com/galaxyproject/galaxy/compare/b9ca3b7c3396...d9f394793897 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c6b593: Migrate API tests in test_jobs.py to use test_hist...
by GitHub 16 Aug '18

16 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c6b593b1ca6efa0ef60b1e9fdbed10022bf9fc4e https://github.com/galaxyproject/galaxy/commit/c6b593b1ca6efa0ef60b1e9fdbed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- Migrate API tests in test_jobs.py to use test_history context. More configurable, better error reporting, cleans up jobs, etc.. Commit: b9ca3b7c339628ac017ffc27a91659dce87c4a96 https://github.com/galaxyproject/galaxy/commit/b9ca3b7c339628ac017ffc27a916… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- Merge pull request #6593 from jmchilton/toward_test_history_cleaning Migrate API tests in test_jobs.py to use test_history context. Compare: https://github.com/galaxyproject/galaxy/compare/318fc0994903...b9ca3b7c3396 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 283947: Update ucsc genome-test server URL.
by GitHub 15 Aug '18

15 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 2839475967320b7d95ade125e542625c6d54c1b9 https://github.com/galaxyproject/galaxy/commit/2839475967320b7d95ade125e542… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Update ucsc genome-test server URL. Commit: 1cd36e3f815b6ad06da7a1aa1ee2c56d67edc36c https://github.com/galaxyproject/galaxy/commit/1cd36e3f815b6ad06da7a1aa1ee2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Bump version; 'patch' since it should be the exact same, as much as anything over the net ever could be\? Commit: 709e49f104e2cba5d180bffb0ed0fee175f5ffba https://github.com/galaxyproject/galaxy/commit/709e49f104e2cba5d180bffb0ed0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Merge pull request #6591 from dannon/ucsc-test-server-domain [18.05] Update UCSC genome-test server URLs Compare: https://github.com/galaxyproject/galaxy/compare/7e445be502a6...709e49f104e2 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 5de98d: add trr datatype
by GitHub 15 Aug '18

15 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5de98d84709bceba887f040760763abf5500b096 https://github.com/galaxyproject/galaxy/commit/5de98d84709bceba887f04076076… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add trr datatype Commit: 0c2dc3aafb684fc13458ba682eb1c46fa6054d7e https://github.com/galaxyproject/galaxy/commit/0c2dc3aafb684fc13458ba682eb1… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: A lib/galaxy/datatypes/test/em.trr Log Message: ----------- add trr example file Commit: 572b9ced2dada0c5a99d52f6de3886ad85b9d368 https://github.com/galaxyproject/galaxy/commit/572b9ced2dada0c5a99d52f6de38… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- no edam format know yet Commit: e42829f03604c8ba0d4a467027c3c3eb689e8395 https://github.com/galaxyproject/galaxy/commit/e42829f03604c8ba0d4a467027c3… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- register datatype Commit: 318fc0994903d3598d9a62e1c8718cb7cde53bfe https://github.com/galaxyproject/galaxy/commit/318fc0994903d3598d9a62e1c871… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/em.trr Log Message: ----------- Merge pull request #6597 from bgruening/trr add trr datatype Compare: https://github.com/galaxyproject/galaxy/compare/ef0a51537e56...318fc0994903 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 3f032f: Rework and simplify data manager testing
by GitHub 15 Aug '18

15 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f032f6c383b108946f77f8fd6b7a02e98d474e1 https://github.com/galaxyproject/galaxy/commit/3f032f6c383b108946f77f8fd6b7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M scripts/functional_tests.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- Rework and simplify data manager testing We don't rely on TwillTestCase anymore, that is now exclusively used by ShedTwillTestCase. Then I've just re-used the infrastructure of ToolsTestCase for discovering tests, while making sure that we do use an admin API key during testing. Commit: e21d94298d5d215a0f4f31dae26848388c593590 https://github.com/galaxyproject/galaxy/commit/e21d94298d5d215a0f4f31dae268… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Look in self.tool_dir if repository_dir is not available Commit: ef0a51537e56e3257532df258494a00a8f7c2506 https://github.com/galaxyproject/galaxy/commit/ef0a51537e56e3257532df258494… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/verify/interactor.py M scripts/functional_tests.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- Merge pull request #6595 from mvdbeek/modernize_data_manager_testing_strip_twill Modernize data manager testing and strip twill Compare: https://github.com/galaxyproject/galaxy/compare/55756ba12de6...ef0a51537e56 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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galaxy-commits August 2018