Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 355b48c361e68a7d9fbe9fe86de7aa2313e5d608
https://github.com/galaxyproject/galaxy/commit/355b48c361e68a7d9fbe9fe86de7…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-12-10 (Mon, 10 Dec 2018)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/util/handlers.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/workflow/scheduling_manager.py
M test/unit/jobs/test_job_configuration.py
M test/unit/tools/test_actions.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Make handler assignment configurable in preparation for new assignment
methods.
Commit: 10c45705bca081c336214b08fcc84d209b19b345
https://github.com/galaxyproject/galaxy/commit/10c45705bca081c336214b08fcc8…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-12-10 (Mon, 10 Dec 2018)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/util/facts.py
M lib/galaxy/util/handlers.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/workflow/scheduling_manager.py
A test/unit/jobs/handler_template_job_conf.xml
M test/unit/jobs/test_job_configuration.py
Log Message:
-----------
Unit tests and fixes for bugs discovered while testing.
Commit: 1fb8203a0c1f6f941e0b13fa6357ec04ea677ffb
https://github.com/galaxyproject/galaxy/commit/1fb8203a0c1f6f941e0b13fa6357…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-12-10 (Mon, 10 Dec 2018)
Changed paths:
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
M config/workflow_schedulers_conf.xml.sample
M doc/source/admin/galaxy_options.rst
M doc/source/admin/jobs.md
M doc/source/admin/scaling.md
M lib/galaxy/jobs/manager.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
-----------
Handler assignment documentation.
Commit: 40f776afde460759b5d682c19ef698fefd2d4388
https://github.com/galaxyproject/galaxy/commit/40f776afde460759b5d682c19ef6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-12-11 (Tue, 11 Dec 2018)
Changed paths:
M lib/galaxy/jobs/manager.py
M lib/galaxy/util/handlers.py
M test/unit/jobs/handler_template_job_conf.xml
M test/unit/jobs/test_job_configuration.py
Log Message:
-----------
Fix tests broken with changes to job_conf.xml.sample_advanced, fix the
broken direct handler assignment method, document the new handler
assignment methods for future method authors. Ensure that enqueue does
its best to return a handler (if known).
Commit: 4a006335ac4ac84a69b5cb1f851e3e63400443ae
https://github.com/galaxyproject/galaxy/commit/4a006335ac4ac84a69b5cb1f851e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-12-11 (Tue, 11 Dec 2018)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Fix default job config (no job_conf.xml).
Commit: e9aec176fac8bb3681ea533be6178ffd43c3bf4d
https://github.com/galaxyproject/galaxy/commit/e9aec176fac8bb3681ea533be617…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-12-11 (Tue, 11 Dec 2018)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Fixes for workflow scheduling tests.
Commit: 7bed9f03180826f7c7f99b12b08bcb265867217b
https://github.com/galaxyproject/galaxy/commit/7bed9f03180826f7c7f99b12b08b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-12-12 (Wed, 12 Dec 2018)
Changed paths:
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
M config/workflow_schedulers_conf.xml.sample
M doc/source/admin/galaxy_options.rst
M doc/source/admin/jobs.md
M doc/source/admin/scaling.md
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/util/facts.py
M lib/galaxy/util/handlers.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/workflow/scheduling_manager.py
A test/unit/jobs/handler_template_job_conf.xml
M test/unit/jobs/test_job_configuration.py
M test/unit/tools/test_actions.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Merge pull request #7091 from natefoo/handler-assignment-fixes
Configurable job/workflow handler assignment methods
Compare: https://github.com/galaxyproject/galaxy/compare/1fd3fccb216b...7bed9f031808
**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.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0c145b3326f2476b05ed8ca7ee66d754099a452f
https://github.com/galaxyproject/galaxy/commit/0c145b3326f2476b05ed8ca7ee66…
Author: thobalose <lose.thoba(a)gmail.com>
Date: 2018-10-18 (Thu, 18 Oct 2018)
Changed paths:
M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/neo/templates/neo.mako
Log Message:
-----------
Updated Neo4j IE to 3.1.9
Commit: 2da38803a3bc12a19e1fa53a1e8cc9e9448eb1b6
https://github.com/galaxyproject/galaxy/commit/2da38803a3bc12a19e1fa53a1e8c…
Author: thobalose <lose.thoba(a)gmail.com>
Date: 2018-10-18 (Thu, 18 Oct 2018)
Changed paths:
M lib/galaxy/visualization/plugins/interactive_environments.py
Log Message:
-----------
Catering for shlex.split(cmd_inject) behaviour
Commit: 1fd3fccb216bcfab298e2cfd812f2ec3b3e45afe
https://github.com/galaxyproject/galaxy/commit/1fd3fccb216bcfab298e2cfd812f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-12-12 (Wed, 12 Dec 2018)
Changed paths:
M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M lib/galaxy/visualization/plugins/interactive_environments.py
Log Message:
-----------
Merge pull request #6897 from thobalose/neo4j-ie
Catered for shlex.split(command_inject) and updated Neo4j IE to v3.1.9
Compare: https://github.com/galaxyproject/galaxy/compare/bf550da2afe9...1fd3fccb216b
**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.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 952fdac419e9b4123c158fd088f90a9a09bc7fd3
https://github.com/galaxyproject/galaxy/commit/952fdac419e9b4123c158fd088f9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-09-10 (Mon, 10 Sep 2018)
Changed paths:
R tools/data_source/bed_convert.xml
Log Message:
-----------
Remove unused and broken tool
Commit: f865e8359fa6c8d599011edcea61a2a728afb9ea
https://github.com/galaxyproject/galaxy/commit/f865e8359fa6c8d599011edcea61…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-09-10 (Mon, 10 Sep 2018)
Changed paths:
M config/job_resource_params_conf.xml.sample
M config/workflow_resource_params_conf.xml.sample
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/functional/tools/for_workflows/head.xml
M test/unit/tools/test_wrappers.py
M tools/data_source/genbank.xml
M tools/data_source/upload.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/CreateInterval.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/changeCase.xml
M tools/filters/fileGrep.xml
M tools/filters/fixedValueColumn.xml
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/grep.xml
M tools/filters/headWrapper.xml
M tools/filters/randomlines.xml
M tools/filters/remove_beginning.xml
M tools/filters/tailWrapper.xml
M tools/filters/wig_to_bigwig.xml
M tools/maf/vcf_to_maf_customtrack.xml
M tools/metag_tools/blat_wrapper.xml
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.xml
M tools/plotting/bar_chart.xml
M tools/plotting/boxplot.xml
M tools/solid_tools/maq_cs_wrapper.xml
M tools/sr_mapping/PerM.xml
M tools/sr_mapping/bfast_wrapper.xml
M tools/stats/filtering.xml
M tools/stats/gsummary.xml
M tools/stats/gsummary.xml.groups
Log Message:
-----------
Deprecate `size` attribute of `<param/>` and remove it from tools
Also:
- dos2unix test/functional/tools/for_workflows/head.xml
- Single-quote text and data params in `<command/>`
- Remove deprecated `interpreter` attribute of `<command />`
Commit: bf550da2afe94ad53aae71e3d930a49cb98558a4
https://github.com/galaxyproject/galaxy/commit/bf550da2afe94ad53aae71e3d930…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-12-12 (Wed, 12 Dec 2018)
Changed paths:
M config/job_resource_params_conf.xml.sample
M config/workflow_resource_params_conf.xml.sample
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/functional/tools/for_workflows/head.xml
M test/unit/tools/test_wrappers.py
R tools/data_source/bed_convert.xml
M tools/data_source/genbank.xml
M tools/data_source/upload.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/CreateInterval.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/changeCase.xml
M tools/filters/fileGrep.xml
M tools/filters/fixedValueColumn.xml
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/grep.xml
M tools/filters/headWrapper.xml
M tools/filters/randomlines.xml
M tools/filters/remove_beginning.xml
M tools/filters/tailWrapper.xml
M tools/filters/wig_to_bigwig.xml
M tools/maf/vcf_to_maf_customtrack.xml
M tools/metag_tools/blat_wrapper.xml
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.xml
M tools/plotting/bar_chart.xml
M tools/plotting/boxplot.xml
M tools/solid_tools/maq_cs_wrapper.xml
M tools/sr_mapping/PerM.xml
M tools/sr_mapping/bfast_wrapper.xml
M tools/stats/filtering.xml
M tools/stats/gsummary.xml
M tools/stats/gsummary.xml.groups
Log Message:
-----------
Merge pull request #6684 from nsoranzo/deprecate_param_size
Deprecate `size` attribute of `<param/>` and remove it from tools
Compare: https://github.com/galaxyproject/galaxy/compare/d06718ef2420...bf550da2afe9
**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.