- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] aeb05e: Add Makefile target for fetching updated bower dep...
by GitHub 03 Jul '16

03 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aeb05e7645a37ffd5cd60b382a429959fca4a20b https://github.com/galaxyproject/galaxy/commit/aeb05e7645a37ffd5cd60b382a42… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M Makefile Log Message: ----------- Add Makefile target for fetching updated bower dependencies. This mirrors the existing `client` target and serves as top-level documentation for how to perform this action. Commit: 6c995f73fb5bd815c03d1ed2ac9284dac607f483 https://github.com/galaxyproject/galaxy/commit/6c995f73fb5bd815c03d1ed2ac92… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-03 (Sun, 03 Jul 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #2534 from jmchilton/client-install-deps Add Makefile target for fetching updated bower dependencies. Compare: https://github.com/galaxyproject/galaxy/compare/00556bd91275...6c995f73fb5b

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[galaxyproject/galaxy] 3d688e: Allow users to purge datasets by default
by GitHub 01 Jul '16

01 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3d688e6bcf49e15fc12f45590250d34cccd0d8cb https://github.com/galaxyproject/galaxy/commit/3d688e6bcf49e15fc12f45590250… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Allow users to purge datasets by default Commit: 00556bd9127579e7b46811f186a0ed3b40dd4b66 https://github.com/galaxyproject/galaxy/commit/00556bd9127579e7b46811f186a0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-01 (Fri, 01 Jul 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Merge pull request #2553 from natefoo/user-purge-default Allow users to purge datasets by default Compare: https://github.com/galaxyproject/galaxy/compare/537b917b4f56...00556bd91275

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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 27 Jun '16

27 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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