Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
Commit: e14e8a074c1344ab62dae2254f1e4a250e963b22
https://github.com/galaxyproject/galaxy/commit/e14e8a074c1344ab62dae2254f1e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-03-04 (Fri, 04 Mar 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Allow rerun of datasets new yet queued by job manager.
Commit: 0c34d5bd3ff414d6beb669e106306066f663d75f
https://github.com/galaxyproject/galaxy/commit/0c34d5bd3ff414d6beb669e10630…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-03-07 (Mon, 07 Mar 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Merge pull request #1858 from jmchilton/rerun_new_datasets
[16.01] Allow rerun of datasets new yet queued by job manager.
Compare: https://github.com/galaxyproject/galaxy/compare/8905bafe1084...0c34d5bd3ff4
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 12883860be223f0d6c306767c372077ceb644dc1
https://github.com/galaxyproject/usegalaxy-playbook/commit/12883860be223f0d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-03-07 (Mon, 07 Mar 2016)
Changed paths:
M galaxy.yml
M galaxy_configs.yml
M production/group_vars/galaxyservers.yml
M stage/group_vars/galaxyservers.yml
M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2
M templates/supervisor/galaxy.conf.j2
A templates/supervisor/galaxy_datamanager.conf.j2
M templates/supervisor/galaxy_group.conf.j2
M templates/supervisor/galaxy_impersonate.conf.j2
M templates/supervisor/galaxy_installer.conf.j2
M templates/supervisor/galaxy_reports.conf.j2
Log Message:
-----------
Add a paste server just for data manager usage. Also update the supervisor configs to remove egg cruft.
Branch: refs/heads/master
Home: https://github.com/galaxyproject/infrastructure-playbook
Commit: a57836480e80c011f3b1c7d3f9e0cd80f2d98ccd
https://github.com/galaxyproject/infrastructure-playbook/commit/a57836480e8…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-03-07 (Mon, 07 Mar 2016)
Changed paths:
A roles/galaxyprojectdotorg.nginx/README.md
A roles/galaxyprojectdotorg.nginx/defaults/main.yml
A roles/galaxyprojectdotorg.nginx/handlers/main.yml
A roles/galaxyprojectdotorg.nginx/meta/.galaxy_install_info
A roles/galaxyprojectdotorg.nginx/meta/main.yml
A roles/galaxyprojectdotorg.nginx/tasks/apt.yml
A roles/galaxyprojectdotorg.nginx/tasks/epel.yml
A roles/galaxyprojectdotorg.nginx/tasks/main.yml
A roles/galaxyprojectdotorg.nginx/templates/http_options.conf.j2
A roles/galaxyprojectdotorg.nginx/templates/ssl.conf.j2
A roles/galaxyprojectdotorg.postgresql/.gitignore
A roles/galaxyprojectdotorg.postgresql/README.md
A roles/galaxyprojectdotorg.postgresql/defaults/main.yml
A roles/galaxyprojectdotorg.postgresql/files/get_repo_rpm_release.py
A roles/galaxyprojectdotorg.postgresql/handlers/main.yml
A roles/galaxyprojectdotorg.postgresql/meta/.galaxy_install_info
A roles/galaxyprojectdotorg.postgresql/meta/main.yml
A roles/galaxyprojectdotorg.postgresql/tasks/backup.yml
A roles/galaxyprojectdotorg.postgresql/tasks/debian.yml
A roles/galaxyprojectdotorg.postgresql/tasks/main.yml
A roles/galaxyprojectdotorg.postgresql/tasks/redhat.yml
A roles/galaxyprojectdotorg.postgresql/templates/20ansible_backup.conf.j2
A roles/galaxyprojectdotorg.postgresql/templates/25ansible_postgresql.conf.j2
A roles/galaxyprojectdotorg.postgresql/templates/archive_wal.sh.j2
A roles/galaxyprojectdotorg.postgresql/templates/backup_working_wal.sh.j2
A roles/galaxyprojectdotorg.postgresql/templates/pg_hba.conf.debian.j2
A roles/galaxyprojectdotorg.postgresql/templates/pg_hba.conf.redhat.j2
A roles/galaxyprojectdotorg.postgresql/templates/scheduled_backup.sh.j2
A roles/galaxyprojectdotorg.postgresql/vars/debian.yml
A roles/galaxyprojectdotorg.postgresql/vars/main.yml
A roles/galaxyprojectdotorg.postgresql/vars/redhat.yml
A roles/geerlingguy.repo-epel/README.md
A roles/geerlingguy.repo-epel/defaults/main.yml
A roles/geerlingguy.repo-epel/meta/.galaxy_install_info
A roles/geerlingguy.repo-epel/meta/main.yml
A roles/geerlingguy.repo-epel/tasks/main.yml
A roles/natefoo.postgresql_objects/README.md
A roles/natefoo.postgresql_objects/defaults/main.yml
A roles/natefoo.postgresql_objects/meta/.galaxy_install_info
A roles/natefoo.postgresql_objects/meta/main.yml
A roles/natefoo.postgresql_objects/tasks/main.yml
A taccenv/files/ssl/wildcard_cert.pem
A taccenv/group_vars/statsservers.yml
A taccenv/host_vars/galaxy06.tacc.utexas.edu.yml
M taccenv/inventory
M taccenv/playbook.yml
A taccenv/secret_group_vars/ssl.yml
A taccenv/templates/nginx/graphite.j2
A taccenv/templates/nginx/sentry.j2
Log Message:
-----------
PostgreSQL and nginx setup for graphite and sentry.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f67cbe72d571f87a87e868161650e5965e681881
https://github.com/galaxyproject/galaxy/commit/f67cbe72d571f87a87e868161650…
Author: Martin Cech <cech.marten(a)gmail.com>
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/0051cab4f35240ff8b85f010b1ae…
Author: Martin Cech <cech.marten(a)gmail.com>
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/a49401189735daa55e44dec7af6b…
Author: Nate Coraor <nate(a)bx.psu.edu>
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/4992684d1fc58d4774e5d6a6c1df…
Author: Dave Bouvier <dave(a)bx.psu.edu>
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/dfef64db75c43cd4001a67cf4814…
Author: Martin Cech <cech.marten(a)gmail.com>
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/de70306407c0682834814c479c91…
Author: John Chilton <jmchilton(a)gmail.com>
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/26d5561b4ff48eb770970bee5f2b…
Author: John Chilton <jmchilton(a)gmail.com>
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/e0ce68cc58a6d6eeb306f5c04455…
Author: John Chilton <jmchilton(a)gmail.com>
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/0fbd22c9a30686afe62de1e1f23f…
Author: Martin Cech <cech.marten(a)gmail.com>
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/97793ab81ab5601466fa89bba7b3…
Author: Martin Cech <cech.marten(a)gmail.com>
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/3aa102343436822b0f4cfccc41d3…
Author: John Chilton <jmchilton(a)gmail.com>
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/6824214816baea26be815ca44dd0…
Author: John Chilton <jmchilton(a)gmail.com>
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