April 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 02ffdf: This strips the graphite-specific middleware; stat...
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 02ffdf0be933b972fbd1dcb2a6b2c210331c520c https://github.com/galaxyproject/galaxy/commit/02ffdf0be933b972fbd1dcb2a6b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/special_topics/performance_tracking.rst M doc/source/lib/galaxy.web.framework.middleware.rst M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- This strips the graphite-specific middleware; statistic functionality is provided by the statsd middleware and we don't need two separate mechanisms to maintain. Commit: 9cee8e229836b707eacb4b3d6ae5cae65e4d6589 https://github.com/galaxyproject/galaxy/commit/9cee8e229836b707eacb4b3d6ae5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/webapps/config_manage.py Log Message: ----------- Add sample commentary to the stub in config manage, xref a88e19064a38415d867f4c118dd6938d8e368632 Commit: b7a89eb106b2924b2d0e1db7749db89de46228c9 https://github.com/galaxyproject/galaxy/commit/b7a89eb106b2924b2d0e1db7749d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Config rebuild Commit: a630f13e6d7e9876a3cce2192953c1fe62dc5962 https://github.com/galaxyproject/galaxy/commit/a630f13e6d7e9876a3cce2192953… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 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 Log Message: ----------- More standard spacing in additional config comments just added. Commit: 740e1fc05c78ff6c05ae5d128489f1514c2b8e1f https://github.com/galaxyproject/galaxy/commit/740e1fc05c78ff6c05ae5d128489… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-01 (Tue, 01 May 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/special_topics/performance_tracking.rst M doc/source/lib/galaxy.web.framework.middleware.rst M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6018 from dannon/kill_graphite_middleware This strips the graphite-specific middleware Compare: https://github.com/galaxyproject/galaxy/compare/9f5a1fa9a613...740e1fc05c78

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[galaxyproject/usegalaxy-playbook] 55697c: Update Main
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 55697c27e93dc6b6e3a79dabff46ed50a7a752c5 https://github.com/galaxyproject/usegalaxy-playbook/commit/55697c27e93dc6b6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] 10ea15: Fix missing `from Import Directory` button
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 10ea15079262a41a9e3c895850b111837549c97e https://github.com/galaxyproject/galaxy/commit/10ea15079262a41a9e3c895850b1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Fix missing `from Import Directory` button when `library_import_dir` is set in `config/galaxy.yml`, but `allow_path_paste` is `false`. Reported by @pvanheus. Commit: 1d0c734fcfcfaf54e676c395acdeeab72b16d517 https://github.com/galaxyproject/galaxy/commit/1d0c734fcfcfaf54e676c395acde… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client-production-maps Commit: 68b87a07635f2ca073286fd0efc7d7ad2e6bcda9 https://github.com/galaxyproject/galaxy/commit/68b87a07635f2ca073286fd0efc7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #5797 from nsoranzo/release_18.01_fix_import_directory [18.01] Fix missing `from Import Directory` button Commit: 59002f69e6657c1e7f88f8e3095000136f0ffcf0 https://github.com/galaxyproject/galaxy/commit/59002f69e6657c1e7f88f8e30950… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Fix update_repository when hg repo has local modifications Fix the following traceback: ``` 149.155.222.206 - - [13/Apr/2018:11:04:46 +0100] "GET /admin_toolshed/update_to_changeset_revision?name=deseq2&latest_ctx_rev=14&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&o wner=iuc&changeset_revision=3660c9088494&latest_changeset_revision=d0c39b5e78cf HTTP/1.1" 500 - "https://galaxy.tgac.ac.uk/admin/repositories?__identifer=lhviib0n1kh" "Mozilla/5.0 (X11 ; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36" Traceback (most recent call last): File "lib/galaxy/web/framework/middleware/batch.py", line 75, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/middleware/request_id.py", line 15, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/xforwardedhost.py", line 23, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/translogger.py", line 71, in __call__ return self.application(environ, replacement_start_response) File "lib/galaxy/web/framework/middleware/error.py", line 166, in __call__ response = self.exception_handler(exc_info, environ) File "lib/galaxy/web/framework/middleware/error.py", line 181, in exception_handler get_vars = wsgilib.parse_querystring(environ) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/request.py", line 107, in parse_querystring strict_parsing=False) File "/usr/lib64/python2.7/urlparse.py", line 408, in parse_qsl pairs = [s2 for s1 in qs.split('&') for s2 in s1.split(';')] File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__ app_iter = self.application(environ, sr_checker) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "lib/galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "lib/galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1650, in update_to_changeset_revision hg_util.update_repository(repo, latest_ctx_rev) File "lib/tool_shed/util/hg_util.py", line 460, in update_repository commands.update(get_configured_ui(), repo, rev=ctx_rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/commands.py", line 6973, in update ret = hg.update(repo, rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 680, in update stats = updaterepo(repo, node, False) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 676, in updaterepo labels=['working copy', 'destination']) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1532, in update stats = applyupdates(repo, actions, wc, p2, overwrite, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1196, in applyupdates complete, r = ms.preresolve(f, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 502, in preresolve return self._resolve(True, dfile, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 457, in _resolve labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 680, in premerge return _filemerge(True, repo, mynode, orig, fcd, fco, fca, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 627, in _filemerge r = _premerge(repo, fcd, fco, fca, toolconf, files, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 324, in _premerge r = simplemerge.simplemerge(ui, a, b, c, quiet=True, label=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/simplemerge.py", line 397, in simplemerge out = opener(os.path.basename(local), "w", atomictemp=True) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/scmutil.py", line 530, in __call__ self.audit(path) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 61, in __call__ or _lowerclean(parts[0]) in ('.hg', '.hg.', '') File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 16, in _lowerclean return encoding.hfsignoreclean(s.lower()) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/encoding.py", line 35, in hfsignoreclean if "\xe2" in s or "\xef" in s: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128) ``` Also, use the Mercurial command line interface instead of the internal API, as recommended in https://www.mercurial-scm.org/wiki/MercurialApi . Commit: 19e05677fa5e9a3a5a8947a551369204a00d535c https://github.com/galaxyproject/galaxy/commit/19e05677fa5e9a3a5a8947a55136… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Skip new script tests in dev branch, they are breaking integration suite. Commit: 3e56c24d0a13f4c0c7bac4deb795de163e214e8c https://github.com/galaxyproject/galaxy/commit/3e56c24d0a13f4c0c7bac4deb795… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #5890 from nsoranzo/fix_update_repository [18.01] Fix update_repository when hg repo has local modifications Commit: 1ff16ddfc401ffcf6edf3b9d14585293ced728a4 https://github.com/galaxyproject/galaxy/commit/1ff16ddfc401ffcf6edf3b9d1458… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Exclude only test_grt_export integration test which takes 35' by itself. Commit: c4e1242312702aea4734a5a96a2bcd15b017c2ec https://github.com/galaxyproject/galaxy/commit/c4e1242312702aea4734a5a96a2b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Merge pull request #5893 from martenson/backport-skip [18.01] Skip new script tests in dev branch, breaking integration suite Commit: 3182dfa70e4220621fe5eb85a05b2f5430a31d3d https://github.com/galaxyproject/galaxy/commit/3182dfa70e4220621fe5eb85a05b… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- correct signal num Commit: cd9db0bffa68cec4891f38db77af578757d3b63d https://github.com/galaxyproject/galaxy/commit/cd9db0bffa68cec4891f38db77af… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Provide ToolDataTableManager for backwards compatibility Broken in 7df9dce63d635d66a0a9ce5045135ab49b7ef506 Commit: c85f07cf5fa2452122487cb66c3955fc88c6ea45 https://github.com/galaxyproject/galaxy/commit/c85f07cf5fa2452122487cb66c39… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #5921 from erasche/fix-docs [18.01] correct signal num in docs Commit: fe0a4853b96ddc163ebfb09f961885b88c5577dd https://github.com/galaxyproject/galaxy/commit/fe0a4853b96ddc163ebfb09f9618… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- forgot to document github bug reporter Commit: 393f055a2307f090f71dc2c7750b8487cfafcd96 https://github.com/galaxyproject/galaxy/commit/393f055a2307f090f71dc2c7750b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- Merge pull request #5928 from erasche/document-gh-reporter [18.01] forgot to document github bug reporter Commit: 50f9ca82ba158736e7ed735e3d949a65127a5111 https://github.com/galaxyproject/galaxy/commit/50f9ca82ba158736e7ed735e3d94… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Don't attempt to determine ports at GIE container launch time if they fail to be determined on the first attempt. They'll be determined by the readiness check instead. Commit: a5c75d2f954f697497747412fd2a998fa61019b0 https://github.com/galaxyproject/galaxy/commit/a5c75d2f954f697497747412fd2a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Correct access for FTP files in composite datatype Commit: 36a182a6c8b6e49bfb90bb452e443ccd746758bb https://github.com/galaxyproject/galaxy/commit/36a182a6c8b6e49bfb90bb452e44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Resort to os.path.exists() also for paths not ending in .loc Fix installation of gatk2 iuc's repo, which otherwise does not add the data tables to `config/shed_tool_data_table_conf.xml` . Introduced in commit 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 . Commit: 0c321cb86e8b8658de00169a1e1e675d547efe07 https://github.com/galaxyproject/galaxy/commit/0c321cb86e8b8658de00169a1e1e… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- removed config.ini parameter from cleanup scripts fixes https://github.com/galaxyproject/galaxy/issues/5941 Commit: 2d772d74b940f67f48e46f21270db0362a93276c https://github.com/galaxyproject/galaxy/commit/2d772d74b940f67f48e46f21270d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- Merge pull request #5956 from bernt-matthias/topic/cleanup_for18.01 removed config.ini parameter from cleanup scripts Commit: 3ab2afb5e5bd82b3aa89500b9c2f80913a054316 https://github.com/galaxyproject/galaxy/commit/3ab2afb5e5bd82b3aa89500b9c2f… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- backport move_merge fix from #5922 Commit: d80e60ce74aabe64e131d560085af099d52b81cf https://github.com/galaxyproject/galaxy/commit/d80e60ce74aabe64e131d560085a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #5947 from nsoranzo/release_17.05_fix_gatk2_install [17.05] Resort to os.path.exists() also for paths not ending in .loc Commit: 8e6cdd73aa4d77ad022c97544b5da060e036065e https://github.com/galaxyproject/galaxy/commit/8e6cdd73aa4d77ad022c97544b5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: 9f8021f1b4ecc0e072f6b0b89a457a09feea0ab1 https://github.com/galaxyproject/galaxy/commit/9f8021f1b4ecc0e072f6b0b89a45… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Commit: 88bf6bbdaa2d15355192eb3c9087151f7712209d https://github.com/galaxyproject/galaxy/commit/88bf6bbdaa2d15355192eb3c9087… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #5943 from erasche/fix-ftp-composite-upload [18.01] Correct access for FTP files in composite datatype Commit: 20e9934bc5922f8d20dd31540a4dce9086495832 https://github.com/galaxyproject/galaxy/commit/20e9934bc5922f8d20dd31540a4d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #5958 from abretaud/movemerge1801 [18.01] Backport to 18.01 the move_merge fix from #5922 Commit: e58034b9876d4fb148049b9cc56a7a99473a7531 https://github.com/galaxyproject/galaxy/commit/e58034b9876d4fb148049b9cc56a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Correct examples in dynamic job conf doc, remove handlers section from basic sample job config (defining a single default handler is no longer needed). Fixes #5976. Commit: e68eaeecbf6641d48487b130988b012bcd2202ca https://github.com/galaxyproject/galaxy/commit/e68eaeecbf6641d48487b130988b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #5981 from natefoo/job-doc-fixes [18.01] Minor Job documentation corrections Commit: 1b1962ea490cdf3f7ff97bfc0f570235ef8ad7fc https://github.com/galaxyproject/galaxy/commit/1b1962ea490cdf3f7ff97bfc0f57… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge pull request #5924 from mvdbeek/fix_data_managers [18.01] Provide ToolDataTableManager for backwards compatibility Commit: 7d81d2cfcba070558dbb1cb5e7b5be390e797ff3 https://github.com/galaxyproject/galaxy/commit/7d81d2cfcba070558dbb1cb5e7b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Fix 2 typos in the docs Commit: a7a4e12e79a91a2a17fa86d65077233f8cfcb35c https://github.com/galaxyproject/galaxy/commit/a7a4e12e79a91a2a17fa86d65077… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix collection element count getting lost during collection copies. Commit: d5ec01d5da1dfde88090afec6df958dfa98af21c https://github.com/galaxyproject/galaxy/commit/d5ec01d5da1dfde88090afec6df9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #5986 from nsoranzo/release_17.09_doc_fixes [17.09] Fix 2 typos in the docs Commit: a3e69636662cfeae0ebc1b66fcc03b0b7fe13be8 https://github.com/galaxyproject/galaxy/commit/a3e69636662cfeae0ebc1b66fcc0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: a29770ca554b5aaf8ea6533ee413fed77042a0ea https://github.com/galaxyproject/galaxy/commit/a29770ca554b5aaf8ea6533ee413… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Pin the version of node we use in CI, etc.... Our dependencies won't resolve under node 10 currently (because of upath at least https://github.com/anodynos/upath/blob/master/package.json#L43 but maybe other packages as well). Commit: c7b426089aa7ec0e0ba874e03ed9dad60a9d1909 https://github.com/galaxyproject/galaxy/commit/c7b426089aa7ec0e0ba874e03ed9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #6000 from jmchilton/fix_build_maybe [18.01] Backport #5972 Commit: cbaff1dca2e34cd869227844a04a761332a7eb27 https://github.com/galaxyproject/galaxy/commit/cbaff1dca2e34cd869227844a04a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Correct uWSGI UNIX domain socket syntax. Commit: 9da13d2d3d3a444e9cd45880496c883b30b475b0 https://github.com/galaxyproject/galaxy/commit/9da13d2d3d3a444e9cd45880496c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5990 from jmchilton/collection_count_fix [18.01] Fix collection element count getting lost during collection copies. Commit: 26ab5388ba31de646d365fbc8528a86b7dc7949a https://github.com/galaxyproject/galaxy/commit/26ab5388ba31de646d365fbc8528… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Merge pull request #5930 from natefoo/gie-late-ports [18.01] Only try to determine GIE container ports once at launch, then hand off to readiness check Commit: 103cb51ec368438642504c3f98b76c363db478bb https://github.com/galaxyproject/galaxy/commit/103cb51ec368438642504c3f98b7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #6003 from natefoo/uwsgi-socket-docs [18.01] Correct uWSGI UNIX domain socket syntax in docs Commit: 717e1104c1e32f79b84de6ffbc481b105087f17f https://github.com/galaxyproject/galaxy/commit/717e1104c1e32f79b84de6ffbc48… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-28 (Sat, 28 Apr 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- enable testing for more BAM types Commit: abf23cdc0bb22542577e5ddefac38242c9ddf8ee https://github.com/galaxyproject/galaxy/commit/abf23cdc0bb22542577e5ddefac3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Merge pull request #6010 from bgruening/test_bam_subtypes [18.01] enable testing for more BAM types Commit: fdfe79f67edd3af8967f916badffcd13aadb78d6 https://github.com/galaxyproject/galaxy/commit/fdfe79f67edd3af8967f916badff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Fix library to list of pairs collection builder. Commit: f50fe5d455594996ba4eb900e0adbf1face67de3 https://github.com/galaxyproject/galaxy/commit/f50fe5d455594996ba4eb900e0ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Rebuild client. Commit: b477329842e7209b2fa2b9389e48b0606b7d8824 https://github.com/galaxyproject/galaxy/commit/b477329842e7209b2fa2b9389e48… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/webapps/galaxy/api/history_contents.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #6015 from jmchilton/fix_library_paired [18.01] Fix library to list of pairs collection builder. Commit: 790ec387d7e3bebec66dd19aaa38e16e2d2266c4 https://github.com/galaxyproject/galaxy/commit/790ec387d7e3bebec66dd19aaa38… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- lastz_wrapper_2 no longer requires Galaxy's python env as of version 1.3 Commit: aebc0da8914f5a2dc3fdc7c68805b174d058f56e https://github.com/galaxyproject/galaxy/commit/aebc0da8914f5a2dc3fdc7c68805… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6020 from natefoo/lastz-1.3 [18.01] lastz_wrapper_2 no longer requires Galaxy's python env as of version 1.3 Commit: 44fc5d6ff98fe939c362539382c7f929c0ce8376 https://github.com/galaxyproject/galaxy/commit/44fc5d6ff98fe939c362539382c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/job_conf.xml.sample_basic M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md M doc/source/admin/jobs.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst M lib/galaxy/containers/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/hg_util.py M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh M scripts/common_startup.sh M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M test/integration/test_scripts.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/c5095d1634a9...44fc5d6ff98f

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[galaxyproject/galaxy] 790ec3: lastz_wrapper_2 no longer requires Galaxy's python...
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 790ec387d7e3bebec66dd19aaa38e16e2d2266c4 https://github.com/galaxyproject/galaxy/commit/790ec387d7e3bebec66dd19aaa38… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- lastz_wrapper_2 no longer requires Galaxy's python env as of version 1.3 Commit: aebc0da8914f5a2dc3fdc7c68805b174d058f56e https://github.com/galaxyproject/galaxy/commit/aebc0da8914f5a2dc3fdc7c68805… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6020 from natefoo/lastz-1.3 [18.01] lastz_wrapper_2 no longer requires Galaxy's python env as of version 1.3 Compare: https://github.com/galaxyproject/galaxy/compare/b477329842e7...aebc0da8914f

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[galaxyproject/usegalaxy-playbook] 9e228b: Remove old mothur from Test
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9e228bd2d8ea32395411a57646831592d83dec23 https://github.com/galaxyproject/usegalaxy-playbook/commit/9e228bd2d8ea3239… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 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: ----------- Remove old mothur from Test Commit: e2d9833f7eaef023da4982bdd946ca0cd676f37b https://github.com/galaxyproject/usegalaxy-playbook/commit/e2d9833f7eaef023… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run lastz like a regular tool Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/bc5263adbfdd...…

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[galaxyproject/galaxy] fdfe79: Fix library to list of pairs collection builder.
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: fdfe79f67edd3af8967f916badffcd13aadb78d6 https://github.com/galaxyproject/galaxy/commit/fdfe79f67edd3af8967f916badff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Fix library to list of pairs collection builder. Commit: f50fe5d455594996ba4eb900e0adbf1face67de3 https://github.com/galaxyproject/galaxy/commit/f50fe5d455594996ba4eb900e0ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Rebuild client. Commit: b477329842e7209b2fa2b9389e48b0606b7d8824 https://github.com/galaxyproject/galaxy/commit/b477329842e7209b2fa2b9389e48… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M lib/galaxy/webapps/galaxy/api/history_contents.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #6015 from jmchilton/fix_library_paired [18.01] Fix library to list of pairs collection builder. Compare: https://github.com/galaxyproject/galaxy/compare/abf23cdc0bb2...b477329842e7

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[galaxyproject/usegalaxy-playbook] bc5263: Bring ansible.cfg options from infrastructure-play...
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bc5263adbfddbd642f705f61afb76b0034c0db72 https://github.com/galaxyproject/usegalaxy-playbook/commit/bc5263adbfddbd64… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: A .pass M ansible.cfg Log Message: ----------- Bring ansible.cfg options from infrastructure-playbook to fix missing inheritance_chain lookup plugin error

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[galaxyproject/usegalaxy-playbook] 98e633: Move Test and Main to Stampede2
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 98e633c616037f137d616f70227fd7b4e3736635 https://github.com/galaxyproject/usegalaxy-playbook/commit/98e633c616037f13… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: A env/main/host_vars/login2.stampede2.tacc.utexas.edu.yml R env/main/host_vars/login5.stampede.tacc.utexas.edu.yml M env/main/inventory M env/test/inventory Log Message: ----------- Move Test and Main to Stampede2

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[galaxyproject/usegalaxy-playbook] 89bbee: Move Test to Stampede2
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 89bbee2e9ea7de43739322f9298fb59ab722e1c7 https://github.com/galaxyproject/usegalaxy-playbook/commit/89bbee2e9ea7de43… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: A .ssh-keyboard-interactive A env/test/host_vars/login2.stampede2.tacc.utexas.edu R env/test/host_vars/login5.stampede.tacc.utexas.edu.yml M env/test/inventory Log Message: ----------- Move Test to Stampede2

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[galaxyproject/galaxy] 1f3a8d: Fix typos
by GitHub 30 Apr '18

30 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1f3a8d4954abfc8222976dd2a2bee987936b91c5 https://github.com/galaxyproject/galaxy/commit/1f3a8d4954abfc8222976dd2a2be… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/tool_destinations.yml.sample M lib/galaxy/managers/collections_util.py Log Message: ----------- Fix typos Commit: 0bcb69df456ea903461e712aa8e83b624f779d0e https://github.com/galaxyproject/galaxy/commit/0bcb69df456ea903461e712aa8e8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix link formatting We cannot use backquote characters in the link text, because pandoc generates a broken RST, see https://github.com/jgm/pandoc/issues/3973 Commit: f2ce39323364c9cf578235c00800816b5208956e https://github.com/galaxyproject/galaxy/commit/f2ce39323364c9cf578235c00800… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Small tool XML doc fixes Commit: 479e76ff13c9a2e232efda5b3d3db7b25a2701c3 https://github.com/galaxyproject/galaxy/commit/479e76ff13c9a2e232efda5b3d3d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Add closing old milestone to release issue Commit: 9f5a1fa9a613bfe6d6b49e3460be1a2e15ca6bce https://github.com/galaxyproject/galaxy/commit/9f5a1fa9a613bfe6d6b49e3460be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M config/tool_destinations.yml.sample M lib/galaxy/managers/collections_util.py M lib/galaxy/tools/xsd/galaxy.xsd M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6013 from nsoranzo/misc Documentation and typo fixes Compare: https://github.com/galaxyproject/galaxy/compare/8c152bda45cb...9f5a1fa9a613

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