galaxy-commits June 2016

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[galaxyproject/galaxy] fe22e1: Adds the ability to use the Kubernetes runner with...
by GitHub 30 Jun '16

30 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fe22e1ec44142980d97c3a81391f654e427d50d0 https://github.com/galaxyproject/galaxy/commit/fe22e1ec44142980d97c3a81391f… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds the ability to use the Kubernetes runner with Galaxy being executed inside Kubernetes (uses service account authentication). Commit: ef72b45320a5aeb68e911028e167150c9f0f29cb https://github.com/galaxyproject/galaxy/commit/ef72b45320a5aeb68e911028e167… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-30 (Thu, 30 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds missing parameter specification for k8s_use_service_account Commit: 537b917b4f5625e78393595be469d6e12fc62c31 https://github.com/galaxyproject/galaxy/commit/537b917b4f5625e78393595be469… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-30 (Thu, 30 Jun 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #2578 from phnmnl/feature/serviceAccount Kubernetes runner: authenticate through service account Compare: https://github.com/galaxyproject/galaxy/compare/05066ae655ca...537b917b4f56

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[galaxyproject/galaxy] b54683: Fixes #2442
by GitHub 30 Jun '16

30 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b5468340eed858efb1d4bc81c721e9362a0ff511 https://github.com/galaxyproject/galaxy/commit/b5468340eed858efb1d4bc81c721… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.xml Log Message: ----------- Fixes #2442 Commit: f8fb69c81a7fd3341ecdff72f498526775bf9604 https://github.com/galaxyproject/galaxy/commit/f8fb69c81a7fd3341ecdff72f498… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.xml Log Message: ----------- All the binary datatypes Commit: 05066ae655ca0ae92f14fce02d5a7f17d720b187 https://github.com/galaxyproject/galaxy/commit/05066ae655ca0ae92f14fce02d5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-30 (Thu, 30 Jun 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.xml Log Message: ----------- Merge pull request #2572 from erasche/fix-2442 Fixes #2442 Compare: https://github.com/galaxyproject/galaxy/compare/79bf27e7e8fd...05066ae655ca

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[galaxyproject/galaxy] 14f34a: Writes logs files in UTF-8 to avoid exceptions pro...
by GitHub 29 Jun '16

29 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 14f34a287f8ebfb533c44a7d1d171ee34b46d8d9 https://github.com/galaxyproject/galaxy/commit/14f34a287f8ebfb533c44a7d1d17… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Writes logs files in UTF-8 to avoid exceptions produced when trying to write non-ascii characters present in logs output. Commit: 3431d4b1a9e4b88ec03e9bffc3ea9c63da9fb3ee https://github.com/galaxyproject/galaxy/commit/3431d4b1a9e4b88ec03e9bffc3ea… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Safer version of encoding. Commit: c9b7d9b68a53ffb58ff83ac8e86f8973a40bfe04 https://github.com/galaxyproject/galaxy/commit/c9b7d9b68a53ffb58ff83ac8e86f… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M config/datatypes_conf.xml.sample M config/job_conf.xml.sample_advanced A display_applications/igv/bigwig.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py M run_tests.sh M scripts/set_dataset_sizes.py M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.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/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/library/common/import_datasets_to_histories.mako M tools/filters/sff_extract.py Log Message: ----------- Merge pull request #5 from galaxyproject/dev keeps up to date with main galaxy dev Commit: 79bf27e7e8fdac3b645444036de0e8439e705295 https://github.com/galaxyproject/galaxy/commit/79bf27e7e8fdac3b645444036de0… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #2528 from phnmnl/dev Writes Kubernetes logs files in UTF-8 Compare: https://github.com/galaxyproject/galaxy/compare/097eb49f5711...79bf27e7e8fd

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[galaxyproject/galaxy] 4ea881: Fix old bug in non-allowed_images.yml GIEs
by GitHub 28 Jun '16

28 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 4ea881caa21602c5562224fa268ff87788eee0dd https://github.com/galaxyproject/galaxy/commit/4ea881caa21602c5562224fa268f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix old bug in non-allowed_images.yml GIEs Commit: 1069a69ae08a4a2db609aebb03c4a8fa53162777 https://github.com/galaxyproject/galaxy/commit/1069a69ae08a4a2db609aebb03c4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2550 from erasche/asdf [16.04] Fix old bug in non-allowed_images.yml GIEs Compare: https://github.com/galaxyproject/galaxy/compare/15a4734aed73...1069a69ae08a

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[galaxyproject/galaxy] babe85: Fixes for showing min/max labels in Trackster.
by GitHub 28 Jun '16

28 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: babe85f3dc5ce075c4919e7b9b02639ac18d3bf1 https://github.com/galaxyproject/galaxy/commit/babe85f3dc5ce075c4919e7b9b02… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Fixes for showing min/max labels in Trackster. Commit: 73b0ebfd2742b26fce9657fdee7a30b315723de0 https://github.com/galaxyproject/galaxy/commit/73b0ebfd2742b26fce9657fdee7a… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Remove debugging statements. Commit: 097eb49f5711c63b1c55a2b4c564e2c2b3f57f41 https://github.com/galaxyproject/galaxy/commit/097eb49f5711c63b1c55a2b4c564… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #2555 from jgoecks/trackster-nan-coverage-fix Fixes for showing min/max labels in Trackster. Compare: https://github.com/galaxyproject/galaxy/compare/d944d3cd6561...097eb49f5711

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[galaxyproject/galaxy] 834736: Small run_tests.sh documentation updates.
by GitHub 28 Jun '16

28 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 834736946c1d23cdea3375925534dae449b850df https://github.com/galaxyproject/galaxy/commit/834736946c1d23cdea3375925534… Author: Nick Stoler <nick(a)nstoler.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M run_tests.sh Log Message: ----------- Small run_tests.sh documentation updates. Make clear that run reports are created by default, print the filename. Commit: d944d3cd6561b72bc9c7598a85b0c4ac77f64919 https://github.com/galaxyproject/galaxy/commit/d944d3cd6561b72bc9c7598a85b0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-27 (Mon, 27 Jun 2016) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #2564 from NickSto/run_tests_documentation run_tests.sh: Clarify when/where the report file is created. Compare: https://github.com/galaxyproject/galaxy/compare/f280645ca2a7...d944d3cd6561

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[galaxyproject/galaxy] 26013f: More defensive proxying
by GitHub 26 Jun '16

26 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 26013f24e47f5b9a7bb6353806de6f0b5f825430 https://github.com/galaxyproject/galaxy/commit/26013f24e47f5b9a7bb6353806de… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- More defensive proxying Commit: f280645ca2a7cd088d299a8f447477f1c164add1 https://github.com/galaxyproject/galaxy/commit/f280645ca2a7cd088d299a8f4474… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Merge pull request #2552 from erasche/gie-proxy-issue More defensive GIE Proxying Compare: https://github.com/galaxyproject/galaxy/compare/b8fa771c4ade...f280645ca2a7

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[galaxyproject/galaxy] 15fac1: Fix old bug in non-allowed_images.yml GIEs
by GitHub 26 Jun '16

26 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 15fac1510fe65c943f9c9aa2557b0ff0d06f4690 https://github.com/galaxyproject/galaxy/commit/15fac1510fe65c943f9c9aa2557b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix old bug in non-allowed_images.yml GIEs Commit: b8fa771c4ade9aeb1bb3ca86086b9fffe2d167e4 https://github.com/galaxyproject/galaxy/commit/b8fa771c4ade9aeb1bb3ca86086b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2548 from erasche/gie-uhoh Fix old bug in non-allowed_images.yml GIEs Compare: https://github.com/galaxyproject/galaxy/compare/48af26ebfb11...b8fa771c4ade

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[galaxyproject/galaxy] a0b20a: Initialize objectstore for fix_set_dataset_sizes s...
by GitHub 26 Jun '16

26 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0b20a61a2dd2ed0d11d21c85d31198d37c747b1 https://github.com/galaxyproject/galaxy/commit/a0b20a61a2dd2ed0d11d21c85d31… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/set_dataset_sizes.py Log Message: ----------- Initialize objectstore for fix_set_dataset_sizes script (otherwise it doesn't currently run successfully) Commit: 48af26ebfb11003f1e981c5cd684bcddd9387c16 https://github.com/galaxyproject/galaxy/commit/48af26ebfb11003f1e981c5cd684… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/set_dataset_sizes.py Log Message: ----------- Merge pull request #2544 from dannon/fix_set_dataset_sizes_script Initialize objectstore for fix_set_dataset_sizes script Compare: https://github.com/galaxyproject/galaxy/compare/6552bd71dffb...48af26ebfb11

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[galaxyproject/galaxy] 43a4a4: Add the missing bigwig xml file for the IGV displa...
by GitHub 26 Jun '16

26 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43a4a45cc8c849075b7eb93d3a830b3750252d76 https://github.com/galaxyproject/galaxy/commit/43a4a45cc8c849075b7eb93d3a83… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: A display_applications/igv/bigwig.xml Log Message: ----------- Add the missing bigwig xml file for the IGV display application Commit: 3d6c55d1ce5c2bf693c710ff03942a3157966afd https://github.com/galaxyproject/galaxy/commit/3d6c55d1ce5c2bf693c710ff0394… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Update the sample datatype_conf.xml file for bigwigs in IGV Commit: 6552bd71dffb1cc75f51bd15eca46064f06d7517 https://github.com/galaxyproject/galaxy/commit/6552bd71dffb1cc75f51bd15eca4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M config/datatypes_conf.xml.sample A display_applications/igv/bigwig.xml Log Message: ----------- Merge pull request #2545 from dpryan79/igv_bigwig bigWig files displayed in IGV Compare: https://github.com/galaxyproject/galaxy/compare/7a5726649d09...6552bd71dffb

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galaxy-commits June 2016