- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] f23d6f: Updated Main (last night, forgot to commit)
by GitHub 12 May '16

12 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f23d6f207c8703a995805fdf28f9e84eac2a925c https://github.com/galaxyproject/usegalaxy-playbook/commit/f23d6f207c8703a9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Updated Main (last night, forgot to commit) Commit: 2ba1cc64570ed7ef9c159ae2ec54bb8c9cf74162 https://github.com/galaxyproject/usegalaxy-playbook/commit/2ba1cc64570ed7ef… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs from Main Commit: 65cd45a384f96edf980db55af5ae6d84ac9ffb68 https://github.com/galaxyproject/usegalaxy-playbook/commit/65cd45a384f96edf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Fix deeptools destinations, also add LD_LIBRARY_PATH for CloudMap to use rpy/R Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/89ad6d275775...…

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[galaxyproject/galaxy] 8255e7: Do not pollute param_dict with a non JSONifiable d...
by GitHub 12 May '16

12 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 8255e722cd21bb1cee594db3212657c6a22aa730 https://github.com/galaxyproject/galaxy/commit/8255e722cd21bb1cee594db32126… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Do not pollute param_dict with a non JSONifiable dict When running a data manager with a dataset parameter, the job fails with the following backtrace: Traceback (most recent call last): File "/opt/galaxy/lib/galaxy/jobs/runners/__init__.py", line 166, in prepare_job job_wrapper.prepare() File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 885, in prepare tool_evaluator.set_compute_environment( compute_environment, get_special=get_special ) File "/opt/galaxy/lib/galaxy/tools/evaluation.py", line 107, in set_compute_environment self.tool.exec_before_job( self.app, inp_data, out_data, param_dict ) File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1956, in exec_before_job out.write( json.dumps( (json_params) ).encode('utf8') ) File "/usr/lib/python2.7/json/__init__.py", line 243, in dumps return _default_encoder.encode(obj) File "/usr/lib/python2.7/json/encoder.py", line 207, in encode chunks = self.iterencode(o, _one_shot=True) File "/usr/lib/python2.7/json/encoder.py", line 270, in iterencode return _iterencode(o, 0) TypeError: keys must be a string The bug was introduced in PR #2029. Commit: e28d305f3cda4377325190363057431f1f4f4d46 https://github.com/galaxyproject/galaxy/commit/e28d305f3cda4377325190363057… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #2345 from nsoranzo/release_16.04_fix_for_2029 [16.04] Do not pollute param_dict with a non JSONifiable dict Compare: https://github.com/galaxyproject/galaxy/compare/013813691ac1...e28d305f3cda

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[galaxyproject/galaxy] 366056: Rebuild following client libs update
by GitHub 12 May '16

12 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 366056c0b70a748f680e4fb8ca8c04565129af2b https://github.com/galaxyproject/galaxy/commit/366056c0b70a748f680e4fb8ca8c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild following client libs update

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[galaxyproject/galaxy] 19a167: UI: minor updates to libraries
by GitHub 12 May '16

12 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19a1679c94ca0a571da0453022aae15a0fce2b44 https://github.com/galaxyproject/galaxy/commit/19a1679c94ca0a571da0453022aa… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js Log Message: ----------- UI: minor updates to libraries Commit: bab9e44db17ff8871567b6d1933d1990ee7f1af9 https://github.com/galaxyproject/galaxy/commit/bab9e44db17ff8871567b6d1933d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M static/maps/libs/bootstrap-tour.js.map M static/maps/libs/d3.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/d3.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js Log Message: ----------- (re-build client) Commit: af15f55ea9c0e511c10e1e3b0bb45c90741c3ecf https://github.com/galaxyproject/galaxy/commit/af15f55ea9c0e511c10e1e3b0bb4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M client/bower.json M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/underscore.js M static/maps/libs/backbone.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/underscore.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/libs/backbone.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/underscore.js Log Message: ----------- UI: major library updates jquery 1.12.3 jquery-migrate 1.4.0 ravenjs 3.0.3 requirejs 2.2.0 tracekit 0.4.3 underscore 1.8.3 backbone 1.3.3 bootstrap-tour 0.10.3 d3 3.5.17 Commit: 7afb7616ff4ec362b34978352ac50c132f530c56 https://github.com/galaxyproject/galaxy/commit/7afb7616ff4ec362b34978352ac5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M test/qunit/tests/form_tests.js Log Message: ----------- Tests: send empty obj to qunit/form_tests `null` caused a script error in require. Commit: 0844852388a16f737557ae58b7a7dd66f43656f0 https://github.com/galaxyproject/galaxy/commit/0844852388a16f737557ae58b7a7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.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/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js Log Message: ----------- UI: remove deprecated jQuery.size() (from selected scripts) Commit: 54f25f262cdd2242e61342521c5643af037149c7 https://github.com/galaxyproject/galaxy/commit/54f25f262cdd2242e61342521c56… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M Makefile R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R config/plugins/visualizations/graphview/static/graphview.js R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js R config/plugins/visualizations/graphview/templates/graphview.mako Log Message: ----------- (merge conflicts) Commit: ecfbf53e6600c8590d3e9fcec9022bf540339985 https://github.com/galaxyproject/galaxy/commit/ecfbf53e6600c8590d3e9fcec902… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M static/maps/mvc/history/history-model.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/history/history-model.js Log Message: ----------- (merge conflicts) Commit: ab05091379463cf6e3d9c416cd601051aacceabd https://github.com/galaxyproject/galaxy/commit/ab05091379463cf6e3d9c416cd60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M client/bower.json M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M static/maps/libs/backbone.js.map M static/maps/libs/bootstrap-tour.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/libs/underscore.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map 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/libs/backbone.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/libs/underscore.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M test/qunit/tests/form_tests.js Log Message: ----------- Merge pull request #2328 from carlfeberhard/client.libs-update Client library updates Compare: https://github.com/galaxyproject/galaxy/compare/09e8f0ab9b83...ab0509137946

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[galaxyproject/galaxy] 7e63ae: Update qunit and sinon
by GitHub 11 May '16

11 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7e63ae66cd93d2cf046484cfa07cf6453656d8c1 https://github.com/galaxyproject/galaxy/commit/7e63ae66cd93d2cf046484cfa07c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M client/galaxy/scripts/utils/metrics-logger.js M static/maps/utils/metrics-logger.js.map M static/scripts/utils/metrics-logger.js M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.14.0.css R test/qunit/test-libs/qunit-1.14.0.js A test/qunit/test-libs/qunit-1.23.1.css A test/qunit/test-libs/qunit-1.23.1.js A test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-1.9.1.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Update qunit and sinon Commit: b7dc5cdf8f66f964e17ed41564b410df97bea9d0 https://github.com/galaxyproject/galaxy/commit/b7dc5cdf8f66f964e17ed41564b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M test/qunit/tests/page_tests.js Log Message: ----------- Fix page test Commit: 74a53c4ebd99fe928ef92e89dba5034945724e5e https://github.com/galaxyproject/galaxy/commit/74a53c4ebd99fe928ef92e89dba5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M test/qunit/test-common.js Log Message: ----------- QUnit can't be shim/init'd since it's a proper AMD module including a define. Commit: 6e5aea08c49603c415ac58f8edf6608f03ca54c3 https://github.com/galaxyproject/galaxy/commit/6e5aea08c49603c415ac58f8edf6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M test/qunit/tests/metrics-logger.js Log Message: ----------- Remove unnecessary MockStorage from Metrics test Commit: 468f17418e9445a18d8b2c2c62fe1d884c331fa4 https://github.com/galaxyproject/galaxy/commit/468f17418e9445a18d8b2c2c62fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M test/qunit/tests/list-of-pairs-collection-creator.js Log Message: ----------- Fix collection test Commit: 09e8f0ab9b838025b5c9b4e9936774018cf789da https://github.com/galaxyproject/galaxy/commit/09e8f0ab9b838025b5c9b4e99367… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M client/galaxy/scripts/utils/metrics-logger.js M static/maps/utils/metrics-logger.js.map M static/scripts/utils/metrics-logger.js M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.14.0.css R test/qunit/test-libs/qunit-1.14.0.js A test/qunit/test-libs/qunit-1.23.1.css A test/qunit/test-libs/qunit-1.23.1.js A test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-1.9.1.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/page_tests.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #2338 from guerler/update_qunit_000 Update qunit and sinon Compare: https://github.com/galaxyproject/galaxy/compare/fcc0d123ea4e...09e8f0ab9b83

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[galaxyproject/infrastructure-playbook] d79b82: Swap from testing to stable channel for Grafana (t...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d79b820cac421179516fb5b452d214990fea592a https://github.com/galaxyproject/infrastructure-playbook/commit/d79b820cac4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Swap from testing to stable channel for Grafana (though this commit also disables use of that channel, in lieu of the remote .rpm until the channel is updated) Commit: 6c8914ec1a0300e8338c3ed9342a2a707ad73054 https://github.com/galaxyproject/infrastructure-playbook/commit/6c8914ec1a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Direct rpm grafana installation Commit: e4a6f1c85cfeee1e49c07d2f31fa6a4d76f2eae0 https://github.com/galaxyproject/infrastructure-playbook/commit/e4a6f1c85cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Merge branch 'stats_role' Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/38b3aaf764…

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[galaxyproject/infrastructure-playbook] 6c8914: Direct rpm grafana installation
by GitHub 11 May '16

11 May '16

Branch: refs/heads/stats_role Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6c8914ec1a0300e8338c3ed9342a2a707ad73054 https://github.com/galaxyproject/infrastructure-playbook/commit/6c8914ec1a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Direct rpm grafana installation

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[galaxyproject/usegalaxy-playbook] b14d78: Disable TACC Jetstream until Ceph @ TACC stabilize...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b14d7836394d5515cefd39d88d099c030986ddf6 https://github.com/galaxyproject/usegalaxy-playbook/commit/b14d7836394d5515… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M files/galaxy/test.galaxyproject.org/config/pulsar_jetstream.yml M files/galaxy/usegalaxy.org/config/pulsar_jetstream.yml Log Message: ----------- Disable TACC Jetstream until Ceph @ TACC stabilizes Commit: 21dda40651195a3d7c4d273f0831592e37cf378b https://github.com/galaxyproject/usegalaxy-playbook/commit/21dda40651195a3d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 89ad6d275775a850cf50d43d089c82f30ef303fd https://github.com/galaxyproject/usegalaxy-playbook/commit/89ad6d275775a850… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Multiple multi handlers for Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/f41f0d01033b...…

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[galaxyproject/infrastructure-playbook] d79b82: Swap from testing to stable channel for Grafana (t...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/stats_role Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d79b820cac421179516fb5b452d214990fea592a https://github.com/galaxyproject/infrastructure-playbook/commit/d79b820cac4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M roles/stats/tasks/main.yml Log Message: ----------- Swap from testing to stable channel for Grafana (though this commit also disables use of that channel, in lieu of the remote .rpm until the channel is updated)

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[galaxyproject/infrastructure-playbook] a98bdd: Influx stack packages.
by GitHub 11 May '16

11 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a98bdd24183c8185424265cfa4358dc39880bfd1 https://github.com/galaxyproject/infrastructure-playbook/commit/a98bdd24183… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: A roles/stats/defaults/main.yml A roles/stats/tasks/main.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml M taccenv/playbook.yml Log Message: ----------- Influx stack packages. Commit: 4cb6510b3e5278c55278e72f770e0a95256f9c7e https://github.com/galaxyproject/infrastructure-playbook/commit/4cb6510b3e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/tasks/main.yml A roles/stats/templates/influxdb.conf.j2 A roles/stats/templates/telegraf.conf.j2 Log Message: ----------- Add stats configs, defaults for now. Commit: 52c4b7f3ac2a14367e6e21bfe4a925651ceb3202 https://github.com/galaxyproject/infrastructure-playbook/commit/52c4b7f3ac2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/tasks/main.yml A roles/stats/templates/grafana.conf.j2 M taccenv/group_vars/statsservers.yml A taccenv/templates/supervisor/stats.j2 Log Message: ----------- Supervisor configs and more for stats role. Commit: 4bc99b4dfb69263e7895729dbaa3c0a69b46e2c4 https://github.com/galaxyproject/infrastructure-playbook/commit/4bc99b4dfb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/tasks/main.yml M roles/stats/templates/grafana.conf.j2 M roles/stats/templates/influxdb.conf.j2 M taccenv/templates/supervisor/stats.j2 Log Message: ----------- Stats startup fixes. Commit: d8006eecfab6822ea881bcd5d2d20018e7593992 https://github.com/galaxyproject/infrastructure-playbook/commit/d8006eecfab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml A taccenv/templates/nginx/stats.j2 Log Message: ----------- Basic nginx config for stats.galaxyproject.org Commit: d0bf01aa82c6eedbaadd94720a2ac78ab766cd7d https://github.com/galaxyproject/infrastructure-playbook/commit/d0bf01aa82c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M roles/stats/templates/grafana.conf.j2 M taccenv/playbook.yml A taccenv/secret_group_vars/stats.yml Log Message: ----------- Configure default user, add vault. Commit: c978f4625c72f5b95b898d84d6bf76a71b86a12e https://github.com/galaxyproject/infrastructure-playbook/commit/c978f4625c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: R taccenv/templates/nginx/graphite.j2 M taccenv/templates/nginx/sentry.j2 M taccenv/templates/nginx/stats.j2 Log Message: ----------- Update nginx confs, remove graphite subdomain. is interesting in nginx, it always returns the first server (which was sentry), and http://stats.galaxyproject.org was redirecting to https://sentry.* before this change. Commit: 6094b47bdc5785c8be93c7af38f36741f3d65314 https://github.com/galaxyproject/infrastructure-playbook/commit/6094b47bdc5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M roles/stats/templates/grafana.conf.j2 M roles/stats/templates/telegraf.conf.j2 Log Message: ----------- Connecting all the things. Commit: 38b3aaf764521c812da0f04c58f508c6c86f6a4c https://github.com/galaxyproject/infrastructure-playbook/commit/38b3aaf7645… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: A roles/stats/defaults/main.yml A roles/stats/tasks/main.yml A roles/stats/templates/grafana.conf.j2 A roles/stats/templates/influxdb.conf.j2 A roles/stats/templates/telegraf.conf.j2 M taccenv/group_vars/statsservers.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml M taccenv/playbook.yml A taccenv/secret_group_vars/stats.yml R taccenv/templates/nginx/graphite.j2 M taccenv/templates/nginx/sentry.j2 A taccenv/templates/nginx/stats.j2 A taccenv/templates/supervisor/stats.j2 Log Message: ----------- Merge pull request #8 from galaxyproject/stats_role Stats role Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/2f0cbfceda…

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[galaxyproject/galaxy] fac2ef: Wrap statsd timing middleware more closely around ...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fac2efc4bd6b2214fa6d17e27b43d26fe4de7d37 https://github.com/galaxyproject/galaxy/commit/fac2efc4bd6b2214fa6d17e27b43… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Wrap statsd timing middleware more closely around the core application in an attempt to prevent manipulation of keys it uses in environ Commit: fcc0d123ea4ea04c77dea5d71b3ff3e1fd984cd1 https://github.com/galaxyproject/galaxy/commit/fcc0d123ea4ea04c77dea5d71b3f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2342 from dannon/stats_layering_fix Wrap statsd timing middleware more closely around the core applicatio… Compare: https://github.com/galaxyproject/galaxy/compare/f3e4cd4ddafc...fcc0d123ea4e

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[galaxyproject/usegalaxy-playbook] f41f0d: nginx config fixes for Jupyter changes
by GitHub 11 May '16

11 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f41f0d01033b5b9626190b76b32f83d6b23a102e https://github.com/galaxyproject/usegalaxy-playbook/commit/f41f0d01033b5b96… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M templates/nginx/usegalaxy.j2 Log Message: ----------- nginx config fixes for Jupyter changes

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[galaxyproject/galaxy] bd25ae: Re-fix the bug with multiple preceding '/' charact...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd25ae95f900cef379214caa43c5b0bfc7705baf https://github.com/galaxyproject/galaxy/commit/bd25ae95f900cef379214caa43c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix Commit: 013813691ac1d67a432a267c0c596a8efde611fb https://github.com/galaxyproject/galaxy/commit/013813691ac1d67a432a267c0c59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2339 from natefoo/gie-proxy-path [16.04] Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix Commit: 073f37a81bfd805b4ccf174d40133da7fe78c9a8 https://github.com/galaxyproject/galaxy/commit/073f37a81bfd805b4ccf174d4013… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'release_16.04' into dev Commit: f3e4cd4ddafc8691e7a84d17feba259ad21a6f3d https://github.com/galaxyproject/galaxy/commit/f3e4cd4ddafc8691e7a84d17feba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Make client. Compare: https://github.com/galaxyproject/galaxy/compare/6ca6ba198de0...f3e4cd4ddafc

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[galaxyproject/galaxy] bd25ae: Re-fix the bug with multiple preceding '/' charact...
by GitHub 11 May '16

11 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: bd25ae95f900cef379214caa43c5b0bfc7705baf https://github.com/galaxyproject/galaxy/commit/bd25ae95f900cef379214caa43c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix Commit: 013813691ac1d67a432a267c0c596a8efde611fb https://github.com/galaxyproject/galaxy/commit/013813691ac1d67a432a267c0c59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-11 (Wed, 11 May 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2339 from natefoo/gie-proxy-path [16.04] Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix Compare: https://github.com/galaxyproject/galaxy/compare/d0830e0c226b...013813691ac1

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[galaxyproject/galaxy] 3672ed: UI, history: update using xhr date header
by GitHub 10 May '16

10 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3672eda0ea82ece74dae918503518e0d19c5dee6 https://github.com/galaxyproject/galaxy/commit/3672eda0ea82ece74dae91850351… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.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/history/history-model.js Log Message: ----------- UI, history: update using xhr date header Makes the 'updated since' contents query based on any previous update's ajax Date response header instead of the client time. This may offer more protection against incorrect client time. This works (and may work better than the previous method) because the Date header is floored and not rounded and seems to mark a time before the contents query is made. Resolves #2242 (hopefully) Commit: 5437c9a7d9131fa4748ee7d338d7a01ba5618fec https://github.com/galaxyproject/galaxy/commit/5437c9a7d9131fa4748ee7d338d7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M Makefile Log Message: ----------- (merge conflicts) Commit: 6ca6ba198de0d71652c18ee8007103fdb3fad3d9 https://github.com/galaxyproject/galaxy/commit/6ca6ba198de0d71652c18ee80071… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.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/history/history-model.js Log Message: ----------- Merge pull request #2335 from carlfeberhard/history.updating-sync UI, history: update using xhr date header Compare: https://github.com/galaxyproject/galaxy/compare/75a99eb11235...6ca6ba198de0

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[galaxyproject/galaxy] cd3f28: Unicodify has different semantics to str
by GitHub 10 May '16

10 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd3f28d8a731475158bb97b807cb451929307cd0 https://github.com/galaxyproject/galaxy/commit/cd3f28d8a731475158bb97b807cb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Unicodify has different semantics to str Originally my patch was written with str()'s behaviour in mind. If a value is None, it gets cast. I did not test my patch well enough following @nsoranzo's request to replace with unicodify(). In that case a raw None gets passed to cgi.escape() causing a bug Commit: 75a99eb112355047692a3a97274f552eab58e705 https://github.com/galaxyproject/galaxy/commit/75a99eb112355047692a3a97274f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #2336 from erasche/fix-for-the-nth-bloody-time Unicodify has different semantics to str, causing bug reporter bug Compare: https://github.com/galaxyproject/galaxy/compare/3ac9d2aa0aa2...75a99eb11235

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[galaxyproject/galaxy] 3005bb: Remove SLURM memory limit warning from stderr if t...
by GitHub 10 May '16

10 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 3005bba5e389c86fccabe129326a1f3a675c6911 https://github.com/galaxyproject/galaxy/commit/3005bba5e389c86fccabe129326a… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Remove SLURM memory limit warning from stderr if the job was successful Commit: 338d25403109244f0b228f9a0df23e02e1de7578 https://github.com/galaxyproject/galaxy/commit/338d25403109244f0b228f9a0df2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Use partial messages to match SLURM memory warnings Commit: ad0647d677cb1979b9841cf0c56ba26d7ec5ca34 https://github.com/galaxyproject/galaxy/commit/ad0647d677cb1979b9841cf0c56b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Change elif to if because drmaa_state can be changed inside the if Commit: 0f984d3bfda9efaa6869286b13ff6842a6df67fb https://github.com/galaxyproject/galaxy/commit/0f984d3bfda9efaa6869286b13ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Unicodify pretty datetimes which can contain non-ASCII chars Commit: 41e6f22f338a6323cb48a23454ca95e798385045 https://github.com/galaxyproject/galaxy/commit/41e6f22f338a6323cb48a23454ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2309 from nsoranzo/release_16.01_slurm_mem_limit [16.01] Remove SLURM memory limit warning from stderr if the job was successful Commit: 79dd8c82f034de51531fb843796249e2b21d9d62 https://github.com/galaxyproject/galaxy/commit/79dd8c82f034de51531fb8437962… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-07 (Sat, 07 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #2312 from nsoranzo/release_16.01_fix_makos [16.01] Unicodify pretty datetimes which can contain non-ASCII chars Commit: afe5e0446ea3a943eb69616fda84fc9870c3b584 https://github.com/galaxyproject/galaxy/commit/afe5e0446ea3a943eb69616fda84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_16.01' Compare: https://github.com/galaxyproject/galaxy/compare/e77d3f009a8e...afe5e0446ea3

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[galaxyproject/galaxy] 37c50d: Relax default value acceptance condition
by GitHub 10 May '16

10 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 37c50d076803e5afd59ebd36691a154360464a45 https://github.com/galaxyproject/galaxy/commit/37c50d076803e5afd59ebd36691a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Relax default value acceptance condition Commit: 8ee9ad293790e066b23f205e43559a60110b7d76 https://github.com/galaxyproject/galaxy/commit/8ee9ad293790e066b23f205e4355… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2316 from guerler/fix_accept_000 [16.04] Relax default value acceptance condition Commit: 443a9e281c238121147af6192e92af80fb1eea53 https://github.com/galaxyproject/galaxy/commit/443a9e281c238121147af6192e92… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- fix proxy name Commit: d0830e0c226b6f3ae061b9d9e93556b3d1bc6c7d https://github.com/galaxyproject/galaxy/commit/d0830e0c226b6f3ae061b9d9e935… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge pull request #2333 from bgruening/proxy_fix Fixes the proxy naming Commit: 3ac9d2aa0aa2210959d5977646ba44b82e07adcf https://github.com/galaxyproject/galaxy/commit/3ac9d2aa0aa2210959d5977646ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/74e6d8b5d8e7...3ac9d2aa0aa2

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[galaxyproject/usegalaxy-playbook] 85e298: Update Pulsar
by GitHub 10 May '16

10 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 85e2989a7ded70fd0040f6a409956f9c456e1e6a https://github.com/galaxyproject/usegalaxy-playbook/commit/85e2989a7ded70fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M production/group_vars/pulsarservers.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Pulsar Commit: 1f0b0280019224bd88e17dc2a7a0f51de02fa90e https://github.com/galaxyproject/usegalaxy-playbook/commit/1f0b0280019224bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a573617ae335...…

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[galaxyproject/galaxy] 443a9e: fix proxy name
by GitHub 10 May '16

10 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 443a9e281c238121147af6192e92af80fb1eea53 https://github.com/galaxyproject/galaxy/commit/443a9e281c238121147af6192e92… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- fix proxy name Commit: d0830e0c226b6f3ae061b9d9e93556b3d1bc6c7d https://github.com/galaxyproject/galaxy/commit/d0830e0c226b6f3ae061b9d9e935… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge pull request #2333 from bgruening/proxy_fix Fixes the proxy naming Compare: https://github.com/galaxyproject/galaxy/compare/8ee9ad293790...d0830e0c226b

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[galaxyproject/galaxy] b5c198: Build: remove redundant webpack step in makefile
by GitHub 10 May '16

10 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b5c198a7bcd758935cbec88966cfbbe09e4658eb https://github.com/galaxyproject/galaxy/commit/b5c198a7bcd758935cbec88966cf… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M Makefile M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Build: remove redundant webpack step in makefile Removes the webpack make target and the 'webpack' call from client target. The webpack production build step is already called from the `grunt` step. Commit: 74e6d8b5d8e7c43f063a0b07e2141212495f9e0c https://github.com/galaxyproject/galaxy/commit/74e6d8b5d8e7c43f063a0b07e214… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-10 (Tue, 10 May 2016) Changed paths: M Makefile M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2327 from carlfeberhard/make.client Build: remove redundant webpack step in makefile Compare: https://github.com/galaxyproject/galaxy/compare/3422b46fb48b...74e6d8b5d8e7

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[galaxyproject/galaxy] 41426e: Visualizations: remove graphview
by GitHub 09 May '16

09 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 41426e4a3d67af916e53002566d6361f203ff9f3 https://github.com/galaxyproject/galaxy/commit/41426e4a3d67af916e53002566d6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R config/plugins/visualizations/graphview/static/graphview.js R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js R config/plugins/visualizations/graphview/templates/graphview.mako Log Message: ----------- Visualizations: remove graphview Has been replaced with graphviz. Commit: 3422b46fb48bdf835697bdfd8f5fa4cba8ebe73a https://github.com/galaxyproject/galaxy/commit/3422b46fb48bdf835697bdfd8f5f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R config/plugins/visualizations/graphview/static/graphview.js R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js R config/plugins/visualizations/graphview/templates/graphview.mako Log Message: ----------- Merge pull request #2329 from carlfeberhard/remove.graphview Visualizations: remove graphview Compare: https://github.com/galaxyproject/galaxy/compare/95c28ff46721...3422b46fb48b

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[galaxyproject/infrastructure-playbook] 2f0cbf: Fixes for old tool versions running on Jetstream
by GitHub 09 May '16

09 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2f0cbfcedada677d177c62a4d67c9dc0ab4a7368 https://github.com/galaxyproject/infrastructure-playbook/commit/2f0cbfcedad… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/galaxynodes.yml Log Message: ----------- Fixes for old tool versions running on Jetstream

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[galaxyproject/galaxy] 37c50d: Relax default value acceptance condition
by GitHub 09 May '16

09 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 37c50d076803e5afd59ebd36691a154360464a45 https://github.com/galaxyproject/galaxy/commit/37c50d076803e5afd59ebd36691a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Relax default value acceptance condition Commit: 8ee9ad293790e066b23f205e43559a60110b7d76 https://github.com/galaxyproject/galaxy/commit/8ee9ad293790e066b23f205e4355… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2316 from guerler/fix_accept_000 [16.04] Relax default value acceptance condition Compare: https://github.com/galaxyproject/galaxy/compare/5710506229e1...8ee9ad293790

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[galaxyproject/galaxy] 0f984d: Unicodify pretty datetimes which can contain non-A...
by GitHub 09 May '16

09 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0f984d3bfda9efaa6869286b13ff6842a6df67fb https://github.com/galaxyproject/galaxy/commit/0f984d3bfda9efaa6869286b13ff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Unicodify pretty datetimes which can contain non-ASCII chars Commit: 427804ff823e4b4277e768e1822bd1642c549a1f https://github.com/galaxyproject/galaxy/commit/427804ff823e4b4277e768e1822b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-05 (Thu, 05 May 2016) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Do not sniff one-line files as CSV/TSV Commit: 5bb7c1d448156c1d20f52eaac3fcab4b1a79e0e5 https://github.com/galaxyproject/galaxy/commit/5bb7c1d448156c1d20f52eaac3fc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-07 (Sat, 07 May 2016) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #2317 from nsoranzo/release_16.04_tsv_fix [16.04] Do not sniff one-line files as CSV/TSV Commit: 79dd8c82f034de51531fb843796249e2b21d9d62 https://github.com/galaxyproject/galaxy/commit/79dd8c82f034de51531fb8437962… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-07 (Sat, 07 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #2312 from nsoranzo/release_16.01_fix_makos [16.01] Unicodify pretty datetimes which can contain non-ASCII chars Commit: 5710506229e16a64a6fe35279fb49df5c73bc0ce https://github.com/galaxyproject/galaxy/commit/5710506229e16a64a6fe35279fb4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: templates/show_params.mako Commit: 95c28ff4672116477851db4d1206adfb480f2b16 https://github.com/galaxyproject/galaxy/commit/95c28ff4672116477851db4d1206… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-09 (Mon, 09 May 2016) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/995509776ef0...95c28ff46721

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