Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823
https://github.com/galaxyproject/galaxy/commit/dd77cdb62576a62ea7e8ce8e31d2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-01-25 (Wed, 25 Jan 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/configuration.py
M test/api/test_datatypes.py
Log Message:
-----------
Add API test for converters after toolbox reload
Commit: 78b4f8f7627a63be7ba593109c1ffd36891168ba
https://github.com/galaxyproject/galaxy/commit/78b4f8f7627a63be7ba593109c1f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-01-25 (Wed, 25 Jan 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/queue_worker.py
Log Message:
-----------
Reload converter tools after toolbox reload
Commit: 36ecf28adaa3328cac3248dc7e8c3ef79211c204
https://github.com/galaxyproject/galaxy/commit/36ecf28adaa3328cac3248dc7e8c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-01-25 (Wed, 25 Jan 2017)
Changed paths:
M test/api/test_datatypes.py
Log Message:
-----------
Use CONVERTER_fasta_to_tabular as example converter (thx @jmchilton)
Commit: e4999510ee2bc44802b4891a1a09b00489b01a9c
https://github.com/galaxyproject/galaxy/commit/e4999510ee2bc44802b4891a1a09…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-01-30 (Mon, 30 Jan 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M test/api/test_datatypes.py
Log Message:
-----------
Merge pull request #3486 from mvdbeek/converter_reload
[16.10] BUG: Reload converter tools after toolbox reload
Commit: cc40b9d45514e1388e2d98e676fe5b75b28d6a3e
https://github.com/galaxyproject/galaxy/commit/cc40b9d45514e1388e2d98e676fe…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M lib/galaxy/model/mapping.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
This enforces serial workflow scheduling within the context of a particular history.
Commit: 749a503534033d3260681b75ad829a640d1c4a3b
https://github.com/galaxyproject/galaxy/commit/749a503534033d3260681b75ad82…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Minor typo in sample.
Commit: 8be1429dda7e158601371331494501fd6043a5e0
https://github.com/galaxyproject/galaxy/commit/8be1429dda7e1586013713314945…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Add configuration for history_local_serial_workflow_scheduling
Commit: 2b55fc75ebad92183e78a80b3240f7b978bd448d
https://github.com/galaxyproject/galaxy/commit/2b55fc75ebad92183e78a80b3240…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
Might be more palatable if this is defaulted to false.
Commit: 9a7066c4b4c9f3824257cc00695b87ef9a065c0f
https://github.com/galaxyproject/galaxy/commit/9a7066c4b4c9f3824257cc00695b…
Author: jvolkening <jdv(a)base2bio.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/tools/verify/asserts/xml.py
Log Message:
-----------
fix <is_valid_xml> output test assert check
Commit: 58241e8dcb71500d399dbe2089f5b20f1eb89b53
https://github.com/galaxyproject/galaxy/commit/58241e8dcb71500d399dbe2089f5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Rebuild client for 17.01 with latest node.
Commit: 9dc1bbd3bc4697f5fbf1e183883aba9277058706
https://github.com/galaxyproject/galaxy/commit/9dc1bbd3bc4697f5fbf1e183883a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
Merge pull request #3535 from dannon/minor_fix
[17.01] Rebuild client for 17.01 with latest node.
Commit: 31725972ef9342145effa6ad24d912022afb278c
https://github.com/galaxyproject/galaxy/commit/31725972ef9342145effa6ad24d9…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix conda resolver when conda_auto_init = True and install = False
Conda dependencies were being prematurely installed during installation of repositories from the ToolShed (at the point where we are just trying to list already installed dependencies).
Commit: a121b889ef584086c96c6b9230198b3e2a04d6f6
https://github.com/galaxyproject/galaxy/commit/a121b889ef584086c96c6b923019…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Only read 6 bytes.
Fixes #3529
Commit: c602336cc82fe60c54d10834c26fb8b0eafe81b0
https://github.com/galaxyproject/galaxy/commit/c602336cc82fe60c54d10834c26f…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/jobs.py
Log Message:
-----------
Fix for rerunning a job when the tool does not exist.
Commit: 3858528d90c1380ae33c7e6087ee3ee1a9bb85f9
https://github.com/galaxyproject/galaxy/commit/3858528d90c1380ae33c7e6087ee…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
Merge pull request #3537 from jmchilton/backport_genbank_fix
[17.01] Backport of fix unbounded readline in genbank datatype
Commit: da7fed47445d8d1483eb456f32af19a0b0ff5412
https://github.com/galaxyproject/galaxy/commit/da7fed47445d8d1483eb456f32af…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix wiggle to wiggle2simple1 for Python path changes in #3364.
Fixes #3539. #minor
Commit: 840c3b0fd846ea5fb58fb34378717aeadea7e81a
https://github.com/galaxyproject/galaxy/commit/840c3b0fd846ea5fb58fb3437871…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M test/integration/test_resolvers.py
Log Message:
-----------
Fix integration test for default Conda mapping.
It worked locally simply because I had R already installed on my system globally.
Commit: a7cc18d616a2fe020d1946eac91ab248f9a1c995
https://github.com/galaxyproject/galaxy/commit/a7cc18d616a2fe020d1946eac91a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix tools that use Galaxy sequence utilities for #3364.
Thanks to @peterjc for reporting and @martenson for grepping.
xref #minor #3364
Commit: bb15a431f006dfbe0d9777529300b8e1981fc988
https://github.com/galaxyproject/galaxy/commit/bb15a431f006dfbe0d9777529300…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3540 from jmchilton/wiggle_fix_1701
[17.01] Fix wiggle to wiggle2simple1 for Python path changes in #3364.
Commit: da0affd45d4fb5479d0e0adcc4efa147bee41e63
https://github.com/galaxyproject/galaxy/commit/da0affd45d4fb5479d0e0adcc4ef…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3542 from jmchilton/more_python_preservation
[17.01] Fix tools that use Galaxy sequence utilities for #3364.
Commit: 105557ba35317120af7f241aebec99f43c4c8553
https://github.com/galaxyproject/galaxy/commit/105557ba35317120af7f241aebec…
Author: jvolkening <jdv(a)base2bio.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
A test-data/simple.xml
A test/functional/tools/is_valid_xml.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
added functional test for <is_valid_xml>
Commit: 2322bc1ff59e85fb4f9db281d04b96e124dd73aa
https://github.com/galaxyproject/galaxy/commit/2322bc1ff59e85fb4f9db281d04b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M test/integration/test_resolvers.py
Log Message:
-----------
Merge pull request #3541 from jmchilton/backport_3508
[17.01] Fix integration test for default Conda mapping.
Commit: f1062afa55c486a0b35418bf7e7e988136c78cb6
https://github.com/galaxyproject/galaxy/commit/f1062afa55c486a0b35418bf7e7e…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/jobs.py
Log Message:
-----------
Merge pull request #3538 from blankenberg/fix-rerun-no-tool
[17.01] Fix for rerunning a job when the tool does not exist.
Commit: 0ce7f6897fe7a037ae9ff9a79c082c56fec0e929
https://github.com/galaxyproject/galaxy/commit/0ce7f6897fe7a037ae9ff9a79c08…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
add comments from @mvdbeek
Commit: 961efb4d9af9ea17fbd0f80b7f07158f2cb971ad
https://github.com/galaxyproject/galaxy/commit/961efb4d9af9ea17fbd0f80b7f07…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #3536 from blankenberg/17.01-conda-fix
[17.01] Fix conda resolver when conda_auto_install = True and install = False
Commit: f6919651f8225c2d48c7b2ecb667e365d7be7bf7
https://github.com/galaxyproject/galaxy/commit/f6919651f8225c2d48c7b2ecb667…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M lib/galaxy/tools/verify/asserts/xml.py
A test-data/simple.xml
A test/functional/tools/is_valid_xml.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3530 from jvolkening/release_17.01
fix <is_valid_xml> output test assert check
Commit: b6cd80a5b35938847d4b306501a4e1fc7030c441
https://github.com/galaxyproject/galaxy/commit/b6cd80a5b35938847d4b306501a4…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M lib/galaxy/datatypes/registry.py
M lib/galaxy/queue_worker.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M test/api/test_datatypes.py
Log Message:
-----------
Merge branch 'release_16.10' into release_17.01
Commit: 62e6639d4716462dc4c6d5292c362a4ce0ba8a31
https://github.com/galaxyproject/galaxy/commit/62e6639d4716462dc4c6d5292c36…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M test/api/test_datatypes.py
Log Message:
-----------
Fix import order
Broken in commit dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 .
Need to remove the file from .ci/flake8_lint_include_list.txt
because 'base' is not in application-import-names
Commit: 409ca0a3c7eec50aaaec15215d380ec098ce4ec1
https://github.com/galaxyproject/galaxy/commit/409ca0a3c7eec50aaaec15215d38…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/model/mapping.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Merge pull request #3520 from dannon/history_serial_workflow_scheduling
[17.01] History-local serial workflow scheduling.
Commit: 49970e786fcf2d885b6a81aa61786cba7912f3fe
https://github.com/galaxyproject/galaxy/commit/49970e786fcf2d885b6a81aa6178…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-02-03 (Fri, 03 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M test/api/test_datatypes.py
Log Message:
-----------
Merge pull request #3549 from nsoranzo/release_17.01_fix_import_order
[17.01] Fix import order
Commit: 0b074f3fa55e5e831d761cefe9dadbf2129706a7
https://github.com/galaxyproject/galaxy/commit/0b074f3fa55e5e831d761cefe9da…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-03 (Fri, 03 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/model/mapping.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/workflow/scheduling_manager.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
A test-data/simple.xml
M test/api/test_datatypes.py
A test/functional/tools/is_valid_xml.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge branch 'release_17.01' into dev
Conflicts:
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
Compare: https://github.com/galaxyproject/galaxy/compare/0219e26085e7...0b074f3fa55e
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: 62e6639d4716462dc4c6d5292c362a4ce0ba8a31
https://github.com/galaxyproject/galaxy/commit/62e6639d4716462dc4c6d5292c36…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M test/api/test_datatypes.py
Log Message:
-----------
Fix import order
Broken in commit dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 .
Need to remove the file from .ci/flake8_lint_include_list.txt
because 'base' is not in application-import-names
Commit: 49970e786fcf2d885b6a81aa61786cba7912f3fe
https://github.com/galaxyproject/galaxy/commit/49970e786fcf2d885b6a81aa6178…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-02-03 (Fri, 03 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M test/api/test_datatypes.py
Log Message:
-----------
Merge pull request #3549 from nsoranzo/release_17.01_fix_import_order
[17.01] Fix import order
Compare: https://github.com/galaxyproject/galaxy/compare/409ca0a3c7ee...49970e786fcf
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5b135fdd39466e8cdcad68f481e5489719c6e75a
https://github.com/galaxyproject/galaxy/commit/5b135fdd39466e8cdcad68f481e5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/verify/__init__.py
Log Message:
-----------
Allow decompressing test outputs.
This seems to be needed to test fastq outputs from tools. Gzipped files seem to depend on the file name before compression - so diff compares (even binary ones) do not work. This allows comparing compressed outputs (and it will magically work if the expected file in test-data is compressed or not).
Builds on the awesome work from @mvdbeek in #3512.
Commit: 0219e26085e79a2b4117d84519a3caae7482e9ef
https://github.com/galaxyproject/galaxy/commit/0219e26085e79a2b4117d84519a3…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-02-03 (Fri, 03 Feb 2017)
Changed paths:
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/verify/__init__.py
Log Message:
-----------
Merge pull request #3550 from jmchilton/decompress_test_outputs
Allow decompressing tool test outputs.
Compare: https://github.com/galaxyproject/galaxy/compare/1dbe75ff1d80...0219e26085e7
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: cc40b9d45514e1388e2d98e676fe5b75b28d6a3e
https://github.com/galaxyproject/galaxy/commit/cc40b9d45514e1388e2d98e676fe…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M lib/galaxy/model/mapping.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
This enforces serial workflow scheduling within the context of a particular history.
Commit: 749a503534033d3260681b75ad829a640d1c4a3b
https://github.com/galaxyproject/galaxy/commit/749a503534033d3260681b75ad82…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Minor typo in sample.
Commit: 8be1429dda7e158601371331494501fd6043a5e0
https://github.com/galaxyproject/galaxy/commit/8be1429dda7e1586013713314945…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Add configuration for history_local_serial_workflow_scheduling
Commit: 2b55fc75ebad92183e78a80b3240f7b978bd448d
https://github.com/galaxyproject/galaxy/commit/2b55fc75ebad92183e78a80b3240…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
Might be more palatable if this is defaulted to false.
Commit: 409ca0a3c7eec50aaaec15215d380ec098ce4ec1
https://github.com/galaxyproject/galaxy/commit/409ca0a3c7eec50aaaec15215d38…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/model/mapping.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Merge pull request #3520 from dannon/history_serial_workflow_scheduling
[17.01] History-local serial workflow scheduling.
Compare: https://github.com/galaxyproject/galaxy/compare/b6cd80a5b359...409ca0a3c7ee