Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f67cbe72d571f87a87e868161650e5965e681881 https://github.com/galaxyproject/galaxy/commit/f67cbe72d571f87a87e8681616... Author: Martin Cech <cech.marten(a)gmail.com&gt; Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- revert escaping added in a24e206ff7762d5b86d3dc7240190f043dc532b5 that prevented line endings and spaces to be rendered properly Commit: 0051cab4f35240ff8b85f010b1ae0d66de7273c0 https://github.com/galaxyproject/galaxy/commit/0051cab4f35240ff8b85f010b1... Author: Martin Cech <cech.marten(a)gmail.com&gt; Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge pull request #1830 from martenson/revert-ts-repo-rendering [16.01] revert ts repo long desc escaping Commit: a49401189735daa55e44dec7af6b84a646e8bbc9 https://github.com/galaxyproject/galaxy/commit/a49401189735daa55e44dec7af... Author: Nate Coraor <nate(a)bx.psu.edu&gt; Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Improve dataset error log message Commit: 4992684d1fc58d4774e5d6a6c1df9c193218c460 https://github.com/galaxyproject/galaxy/commit/4992684d1fc58d4774e5d6a6c1... Author: Dave Bouvier <dave(a)bx.psu.edu&gt; Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Hide tools that have been replaced. Commit: dfef64db75c43cd4001a67cf48143e28df3efe60 https://github.com/galaxyproject/galaxy/commit/dfef64db75c43cd4001a67cf48... Author: Martin Cech <cech.marten(a)gmail.com&gt; Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #1836 from natefoo/dataset-error-log [16.01] Improve dataset error log message Commit: de70306407c0682834814c479c91f8b8adc615ce https://github.com/galaxyproject/galaxy/commit/de70306407c0682834814c479c... Author: John Chilton <jmchilton(a)gmail.com&gt; Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Merge pull request #1837 from davebx/release_16.01 [16.01] Hide tools that have been replaced. Commit: 26d5561b4ff48eb770970bee5f2ba49d425e9902 https://github.com/galaxyproject/galaxy/commit/26d5561b4ff48eb770970bee5f... Author: John Chilton <jmchilton(a)gmail.com&gt; Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Update more scripts to respect GALAXY_VIRTUAL_ENV. Drop explicit sourcing in run_reports and run_tool_shed since they source common_startup. Commit: e0ce68cc58a6d6eeb306f5c0445563e71bcc1d12 https://github.com/galaxyproject/galaxy/commit/e0ce68cc58a6d6eeb306f5c044... Author: John Chilton <jmchilton(a)gmail.com&gt; Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix lack of output when discovering large collections... Example log statement collected for each dataset: ``` galaxy.tools.parameters.output_collect DEBUG 2016-03-03 11:47:31,302 (8) Created dynamic collection dataset for path [/home/john/workspace/galaxy/database/job_working_directory/000/8/oe2_ie2.fq] with element identifier [oe2:ie2] for output [list_output]. ``` Commit: 0fbd22c9a30686afe62de1e1f23ff309dd6374a8 https://github.com/galaxyproject/galaxy/commit/0fbd22c9a30686afe62de1e1f2... Author: Martin Cech <cech.marten(a)gmail.com&gt; Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #1852 from jmchilton/dataset_collection_log [16.01] Fix lack of log output when discovering large collections... Commit: 97793ab81ab5601466fa89bba7b3250118e95de4 https://github.com/galaxyproject/galaxy/commit/97793ab81ab5601466fa89bba7... Author: Martin Cech <cech.marten(a)gmail.com&gt; Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1847 from jmchilton/more_virtualenv_fixes [16.01] Update more scripts to respect GALAXY_VIRTUAL_ENV. Commit: 3aa102343436822b0f4cfccc41d3df146680ad21 https://github.com/galaxyproject/galaxy/commit/3aa102343436822b0f4cfccc41... Author: John Chilton <jmchilton(a)gmail.com&gt; Date: 2016-03-05 (Sat, 05 Mar 2016) Changed paths: M config/tool_conf.xml.main M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M manage_tools.sh M run_reports.sh M run_tool_shed.sh M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_16.01' into dev Commit: 6824214816baea26be815ca44dd0e15a9f665cad https://github.com/galaxyproject/galaxy/commit/6824214816baea26be815ca44d... Author: John Chilton <jmchilton(a)gmail.com&gt; Date: 2016-03-05 (Sat, 05 Mar 2016) Changed paths: M config/tool_conf.xml.main M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/parameters/output_collect.py M manage_tools.sh M run_reports.sh M run_tool_shed.sh M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge pull request #1876 from jmchilton/merge_16.01_0 Merge latest 16.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/2e4f8f75dcfa...6824214816ba