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
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:
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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:
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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:
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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:
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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:
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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
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
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