galaxy-commits March 2016

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208 discussions

[galaxyproject/galaxy] e14e8a: Allow rerun of datasets new yet queued by job mana...
by GitHub 07 Mar '16

07 Mar '16

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

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[galaxyproject/usegalaxy-playbook] 379437: Missed one of the renames
by GitHub 07 Mar '16

07 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 379437397d33dc78c9e601925c4e95e7ce270365 https://github.com/galaxyproject/usegalaxy-playbook/commit/379437397d33dc78… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Missed one of the renames

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[galaxyproject/usegalaxy-playbook] 128838: Add a paste server just for data manager usage. Al...
by GitHub 07 Mar '16

07 Mar '16

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.

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[galaxyproject/usegalaxy-playbook] b53ef9: Integrated tool panel changes from Test
by GitHub 07 Mar '16

07 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b53ef9ab81e7826a68619a09893a37cbe042ac87 https://github.com/galaxyproject/usegalaxy-playbook/commit/b53ef9ab81e7826a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml Log Message: ----------- Integrated tool panel changes from Test

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[galaxyproject/galaxy] 774487: Fix citation-model to fail silently/gracefully whe...
by GitHub 07 Mar '16

07 Mar '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 774487ddcc9c0e793b6b15b26c971c3df5822644 https://github.com/galaxyproject/galaxy/commit/774487ddcc9c0e793b6b15b26c97… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried Commit: d225aebc8879b3e96963724d3b5b11aec1d50ed5 https://github.com/galaxyproject/galaxy/commit/d225aebc8879b3e96963724d3b5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #1884 from carlfeberhard/release_15.10 [15.10] Fix citation-model to fail silently/gracefully Compare: https://github.com/galaxyproject/galaxy/compare/b5949bcbbfbc...d225aebc8879

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[galaxyproject/infrastructure-playbook] a57836: PostgreSQL and nginx setup for graphite and sentry...
by GitHub 07 Mar '16

07 Mar '16

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.

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[galaxyproject/galaxy] 7e5d99: Update check_python.py now dropping Python 2.6
by GitHub 07 Mar '16

07 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7e5d99ebb2b3bb98b96a43cfb9ea82827a96dd23 https://github.com/galaxyproject/galaxy/commit/7e5d99ebb2b3bb98b96a43cfb9ea… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M scripts/check_python.py Log Message: ----------- Update check_python.py now dropping Python 2.6 Closes #1596 Commit: cff3eb8073ea07165aa8d6d60405c25ebe63a40a https://github.com/galaxyproject/galaxy/commit/cff3eb8073ea07165aa8d6d60405… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M scripts/check_python.py Log Message: ----------- Merge pull request #1883 from peterjc/drop26 Update check_python.py now dropping Python 2.6 Compare: https://github.com/galaxyproject/galaxy/compare/6824214816ba...cff3eb8073ea

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[galaxyproject/galaxy] 0445fc: Add workflow building mode check to collection par...
by GitHub 06 Mar '16

06 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 0445fcda51cad08a0b2969140b48948a9e7d759b https://github.com/galaxyproject/galaxy/commit/0445fcda51cad08a0b2969140b48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add workflow building mode check to collection parameter handling Commit: 8905bafe10845545bedbd1c6b9e758e1b9523b4d https://github.com/galaxyproject/galaxy/commit/8905bafe10845545bedbd1c6b9e7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-06 (Sun, 06 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1859 from guerler/fix_collection_000 [16.01] Add workflow building mode check to collection parameter handling Compare: https://github.com/galaxyproject/galaxy/compare/97793ab81ab5...8905bafe1084

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[galaxyproject/galaxy] f67cbe: revert escaping added in a24e206ff7762d5b86d3dc724...
by GitHub 05 Mar '16

05 Mar '16

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

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[galaxyproject/galaxy] a324f7: Do not access the history when loading the workflo...
by GitHub 05 Mar '16

05 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a324f7febd242ea707495c2dd37ec4f2720f0eb9 https://github.com/galaxyproject/galaxy/commit/a324f7febd242ea707495c2dd37e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Do not access the history when loading the workflow editor Commit: 4f7706207f736fc1f34321b37c41ae99e3dfa3c5 https://github.com/galaxyproject/galaxy/commit/4f7706207f736fc1f34321b37c41… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Undo signature consistency change Commit: 2e4f8f75dcfab794d17f3fe49e324cf1ceee6d94 https://github.com/galaxyproject/galaxy/commit/2e4f8f75dcfab794d17f3fe49e32… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-05 (Sat, 05 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1861 from guerler/fix_workflow_loading_001 Do not access the history when loading the workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/9449b4ae204b...2e4f8f75dcfa

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galaxy-commits March 2016