- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] affab0: Simplify item_attrs - eliminate RuntimeException n...
by Nicola Soranzo 14 Feb '19

14 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: affab0138fa9aa56847c1d9f69c7859df3ba3eb8 https://github.com/galaxyproject/galaxy/commit/affab0138fa9aa56847c1d9f69c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/model/item_attrs.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/reports/framework/grids.py Log Message: ----------- Simplify item_attrs - eliminate RuntimeException never caught. Commit: 572d74249ebd84d22bf2a99f40db7b37c01ba5b7 https://github.com/galaxyproject/galaxy/commit/572d74249ebd84d22bf2a99f40db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/model/item_attrs.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/reports/framework/grids.py Log Message: ----------- Eliminate code dup around item_attrs. Commit: 79642f3ff2002981526dd81a6073e109fb2f455f https://github.com/galaxyproject/galaxy/commit/79642f3ff2002981526dd81a6073… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/model/item_attrs.py Log Message: ----------- item_attrs: Refactor _get_annotation_assoc_class out of mixin into standalone method. Commit: 27662005be9edb0639a893766cf678fcf940c76c https://github.com/galaxyproject/galaxy/commit/27662005be9edb0639a893766cf6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/model/item_attrs.py Log Message: ----------- item_attrs: Refactor get_item_annotation_obj out of mixin into standalone method. Commit: 5c35b7b296075409cf3a8a322b16975afd4dfbc8 https://github.com/galaxyproject/galaxy/commit/5c35b7b296075409cf3a8a322b16… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/model/item_attrs.py Log Message: ----------- item_attrs: Refactor more methods out of mixin into standalone method. Commit: 834e9f2edcfd0d2e6685b08d3a50e61c0db2dbbe https://github.com/galaxyproject/galaxy/commit/834e9f2edcfd0d2e6685b08d3a50… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Eliminate mixin use in galaxy.tools.imp_exp. Commit: 0020c7d23297bffc5dad775834b5bb011040873b https://github.com/galaxyproject/galaxy/commit/0020c7d23297bffc5dad775834b5… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M lib/galaxy/model/item_attrs.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/reports/framework/grids.py Log Message: ----------- Merge pull request #7346 from jmchilton/item_attrs_refactor_2 Refactor item_attrs for reuse without mixin inheritance. Compare: https://github.com/galaxyproject/galaxy/compare/110d95531361...0020c7d23297

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[galaxyproject/galaxy] f32085: Drop 'fade in' classes on iframe; prefer static di...
by John Chilton 14 Feb '19

14 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: f3208503f69bae63ef48e18deb85e7aa974e20c5 https://github.com/galaxyproject/galaxy/commit/f3208503f69bae63ef48e18deb85… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js Log Message: ----------- Drop 'fade in' classes on iframe; prefer static display without extra animations and fixes opacity issue from biostar. Commit: bfeb2727573a6c1c77551369bf46acf93d78190b https://github.com/galaxyproject/galaxy/commit/bfeb2727573a6c1c77551369bf46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/style/scss/base.scss Log Message: ----------- drop redundant communication server frame styles. Commit: b29b8b5c17f4126b0af597c0bccac850767f5aff https://github.com/galaxyproject/galaxy/commit/b29b8b5c17f4126b0af597c0bcca… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js Log Message: ----------- Use standard bootstrap classes for sizing here since it's only used in one spot. Commit: 45d06acbc8f31bdeab7b895d3fadf71d4a9aaa84 https://github.com/galaxyproject/galaxy/commit/45d06acbc8f31bdeab7b895d3fad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M client/galaxy/scripts/layout/communication-server-view.js M client/galaxy/style/scss/base.scss Log Message: ----------- Merge pull request #7354 from dannon/comm_server_fixes [19.01] Communication Server Display Fixes Compare: https://github.com/galaxyproject/galaxy/compare/62d8d808eb09...45d06acbc8f3

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[galaxyproject/galaxy] 4427d3: Separate client node version requirement into indi...
by John Chilton 14 Feb '19

14 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4427d3a982cff3321c878543dad72a1611afedac https://github.com/galaxyproject/galaxy/commit/4427d3a982cff3321c878543dad7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: A client/.node_version M scripts/common_startup.sh Log Message: ----------- Separate client node version requirement into individual dotfile for easier reading/use in ansible playbooks Commit: 110d95531361f2e527f13de2e3658c4216b5cbc0 https://github.com/galaxyproject/galaxy/commit/110d95531361f2e527f13de2e365… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: A client/.node_version M scripts/common_startup.sh Log Message: ----------- Merge pull request #7357 from dannon/node-ver-in-dotfile Separate client node version requirement into individual dotfile for … Compare: https://github.com/galaxyproject/galaxy/compare/0e03aea084d0...110d95531361

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[galaxyproject/usegalaxy-playbook] d879b4: Allocate 16GB for:
by Nate Coraor 13 Feb '19

13 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d879b4e3e36186421a88ce8d260cedad18b69bec https://github.com/galaxyproject/usegalaxy-playbook/commit/d879b4e3e3618642… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Allocate 16GB for: - toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4 - toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4 - toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4 Resolves #142.

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[galaxyproject/usegalaxy-playbook] 5c70fd: Update Main
by Nate Coraor 13 Feb '19

13 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5c70fddc6ed2bf5f8baa6d600d8a2266ebe7f5d8 https://github.com/galaxyproject/usegalaxy-playbook/commit/5c70fddc6ed2bf5f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/group_vars/all.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] a10d2c: Add/pin configurable node version to 18.09. Backp...
by Dannon 13 Feb '19

13 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a10d2c51d3e29ceef17b056992f04f98b0f8472c https://github.com/galaxyproject/galaxy/commit/a10d2c51d3e29ceef17b056992f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Add/pin configurable node version to 18.09. Backport/tweak of https://github.com/galaxyproject/galaxy/pull/7220) Commit: 9f501bb2b0bfa5193cd908d5f43bdca9a4bc5a2d https://github.com/galaxyproject/galaxy/commit/9f501bb2b0bfa5193cd908d5f43b… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2019-02-04 (Mon, 04 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar Log Message: ----------- Add datatypes and sniffers for several directory-based mass spectrometry formats: Bruker BAF, Agilent/Bruker YEP, Bruker TDF, Agilent MassHunter, and Waters MassLynx Commit: 68a66f462e007fdbcf8e966fc5cc1a7ea06a8527 https://github.com/galaxyproject/galaxy/commit/68a66f462e007fdbcf8e966fc5cc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- update h5py dependency Commit: d79514b823371c36c12dcbb6aef25a4490cd50ca https://github.com/galaxyproject/galaxy/commit/d79514b823371c36c12dcbb6aef2… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/__init__.py Log Message: ----------- allow assertions on binary inputs Commit: e37036af04ac34dd7c865f5f11ccaa0ee4e17e9a https://github.com/galaxyproject/galaxy/commit/e37036af04ac34dd7c865f5f11cc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A lib/galaxy/tools/verify/asserts/hdf5.py Log Message: ----------- add hdf5 assert tests Commit: db2987b2b21fefad9feb2af0bd4f93b7d490361f https://github.com/galaxyproject/galaxy/commit/db2987b2b21fefad9feb2af0bd4f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A test/functional/tools/validation_hdf5.xml Log Message: ----------- add test tool for new assertions Commit: d4420b75662b7667d430f78be67b09e69037a77b https://github.com/galaxyproject/galaxy/commit/d4420b75662b7667d430f78be67b… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- register new test tool Commit: a00fd508b758fc73aeb537ca98156fff1c7ac14d https://github.com/galaxyproject/galaxy/commit/a00fd508b758fc73aeb537ca9815… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- adopt XSD for new syntax Commit: cb13e56e6bd00a932e9594241fe043f845d4f815 https://github.com/galaxyproject/galaxy/commit/cb13e56e6bd00a932e9594241fe0… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: A test-data/matrix.cool Log Message: ----------- add test-data for new hdf5 based tool test Commit: e9f40f2f95a611f0fab6d81bb225cf409b86f353 https://github.com/galaxyproject/galaxy/commit/e9f40f2f95a611f0fab6d81bb225… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py Log Message: ----------- fix pep8 Commit: 2a97f726cc86d44610738d04755622e8e4b8342a https://github.com/galaxyproject/galaxy/commit/2a97f726cc86d44610738d047556… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- Tweaks to hdf5 testing. - This is in galaxy-lib so h5py import should probably be conditional. - Namespace very generic test functions a bit by adding h5 into the names. - Stricter validation of XSD (the other assertions don't have this but that is problematic on their part), I'm not sure if the docs will render unevenly now though - we may want to revisit that and do this for all the assertions. Commit: 3d4ff4fc372bc6b44b384af944b548915427fda4 https://github.com/galaxyproject/galaxy/commit/3d4ff4fc372bc6b44b384af944b5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge pull request #41 from jmchilton/hdf5_tests Tweaks to hdf5 testing. Commit: 365ac400ae629b415b8ec11a364ec0e4465d1c7f https://github.com/galaxyproject/galaxy/commit/365ac400ae629b415b8ec11a364e… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix lint errors Commit: 413af14bb55d890ca053d08877cee98ab440008f https://github.com/galaxyproject/galaxy/commit/413af14bb55d890ca053d08877ce… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix lint errors Commit: d30852b286b9baba5cf6faffa389db8ec2837114 https://github.com/galaxyproject/galaxy/commit/d30852b286b9baba5cf6faffa389… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/some.wiff.tar Log Message: ----------- Add wiff.tar extension and sniffer Commit: 0a7583b6de024d02b7063fa3f59c7febe63df5f5 https://github.com/galaxyproject/galaxy/commit/0a7583b6de024d02b7063fa3f59c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- More contrast Commit: 87c82595771438b0e8244b32885430e4fe1bab6e https://github.com/galaxyproject/galaxy/commit/87c82595771438b0e8244b328854… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Add box-shadow Commit: 12fde52494541d73da42a41d026c8a0217d7533c https://github.com/galaxyproject/galaxy/commit/12fde52494541d73da42a41d026c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- remove inaccurate comment Commit: dc303f004fc5254f6de14bc29084532d3db98912 https://github.com/galaxyproject/galaxy/commit/dc303f004fc5254f6de14bc29084… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Remove try/except in sniffers Add .d/.raw to file_ext Commit: d36cf51f6b63407fd96e49918fe6092d993275a9 https://github.com/galaxyproject/galaxy/commit/d36cf51f6b63407fd96e49918fe6… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_hdf5.xml Log Message: ----------- change "name" to "key" Commit: b59d76eb4a928af8866275cb91afd583a82fee99 https://github.com/galaxyproject/galaxy/commit/b59d76eb4a928af8866275cb91af… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix emoji tags Commit: dd917099ba43b3d9638c16623ca45bc13edfc9c5 https://github.com/galaxyproject/galaxy/commit/dd917099ba43b3d9638c16623ca4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Only block the single category of C characters that is problematic Co-Authored-By: erasche <hxr(a)hx42.org> Commit: e3f1234b2c1359e4d5353ba0e0b56834a964bb28 https://github.com/galaxyproject/galaxy/commit/e3f1234b2c1359e4d5353ba0e0b5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #7310 from erasche/fix-emoji-tags [19.01] Fix emoji tags Commit: 23d4af5dafbb768ba61c6cf8849cd17087f31520 https://github.com/galaxyproject/galaxy/commit/23d4af5dafbb768ba61c6cf8849c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-06 (Wed, 06 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Revert "Add box-shadow" This reverts commit 87c82595771438b0e8244b32885430e4fe1bab6e. Commit: 8f7263a1dcce4a2d3e5c251e4253dece2998e61d https://github.com/galaxyproject/galaxy/commit/8f7263a1dcce4a2d3e5c251e4253… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd A test-data/matrix.cool M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge pull request #7301 from bgruening/hdf5_tests Add new test syntax specific for HDF5 files Commit: f0026962219ebad2177f57ebee5ae9b837882e60 https://github.com/galaxyproject/galaxy/commit/f0026962219ebad2177f57ebee5a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Merge pull request #7309 from erasche/more-contrast [19.01] More contrast in CSS Commit: f7322d85a317614de1a745da57d5e394b5eb8041 https://github.com/galaxyproject/galaxy/commit/f7322d85a317614de1a745da57d5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2019-02-09 (Sat, 09 Feb 2019) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar A lib/galaxy/datatypes/test/some.wiff.tar Log Message: ----------- Merge pull request #7299 from chambm/feature/rawtar-datatypes Add datatypes and sniffers for tar archives of directory-based MS formats and WIFF/SCAN pairs Commit: 9c9c8a5d50d7c8ae68f34712d0e9b053aed33ea2 https://github.com/galaxyproject/galaxy/commit/9c9c8a5d50d7c8ae68f34712d0e9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7239 from dannon/node_ver_pin_18.09 [18.09] Add/pin configurable node version Commit: b33b06440ffdd7e58b6172315df1e015e4ac0e52 https://github.com/galaxyproject/galaxy/commit/b33b06440ffdd7e58b6172315df1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 21ce99e231af7eaa0c81e3fcc9dae1f857ab1e1c https://github.com/galaxyproject/galaxy/commit/21ce99e231af7eaa0c81e3fcc9da… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar A lib/galaxy/datatypes/test/some.wiff.tar M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M scripts/common_startup.sh A test-data/matrix.cool M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge branch 'release_19.01' into dev Commit: 2f1a0cd2581ced221e8d4d9264cfe386642bdf73 https://github.com/galaxyproject/galaxy/commit/2f1a0cd2581ced221e8d4d9264cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Use brand-secondary for tool form titles in canvas (the workflow editor) Commit: 0e03aea084d05405a2b6c296877dc8513714e004 https://github.com/galaxyproject/galaxy/commit/0e03aea084d05405a2b6c296877d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/brukerbaf.d.tar A lib/galaxy/datatypes/test/some.wiff.tar M lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/hdf5.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M scripts/common_startup.sh A test-data/matrix.cool M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_hdf5.xml Log Message: ----------- Merge pull request #7350 from nsoranzo/merge_19.01 Merge 19.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/4b92f95e87b1...0e03aea084d0

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[galaxyproject/galaxy] d710bb: Discriminate data managers and allow managed testing
by John Chilton 13 Feb '19

13 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: d710bb860b5802a64420eb3d5e1ebac6ac88d4ea https://github.com/galaxyproject/galaxy/commit/d710bb860b5802a64420eb3d5e1e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/loader_directory.py Log Message: ----------- Discriminate data managers and allow managed testing I am not a big fan of the heuristic in which we fall back to loading the data manager tool relative to the data_manager_conf.xml file, but I don't really see a better way here. Commit: 62d8d808eb096daa4c99bdefd3c0aabaa3a59e56 https://github.com/galaxyproject/galaxy/commit/62d8d808eb096daa4c99bdefd3c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #7331 from mvdbeek/test_data_managers [19.01] Discriminate data managers and allow managed testing Compare: https://github.com/galaxyproject/galaxy/compare/b33b06440ffd...62d8d808eb09

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[galaxyproject/usegalaxy-playbook] 11e033: Add support for setting the node version. Temporar...
by Nate Coraor 13 Feb '19

13 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 11e03390e6a5fbf8c587a3ffc2bcddb8808a7b54 https://github.com/galaxyproject/usegalaxy-playbook/commit/11e03390e6a5fbf8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M env/main/group_vars/cvmfsstratum0servers.yml M env/test/group_vars/cvmfsstratum0servers.yml M roles/usegalaxy_cvmfs/tasks/_inc_client_build.yml Log Message: ----------- Add support for setting the node version. Temporarily always run nodeenv. Commit: da59a8276eb31ab231f2106578821d5531bceabc https://github.com/galaxyproject/usegalaxy-playbook/commit/da59a8276eb31ab2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-13 (Wed, 13 Feb 2019) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/0e7966e82ed6...…

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[galaxyproject/usegalaxy-playbook] 0e7966: 1. Fix a bug in the Bridges dynamic rule that woul...
by Nate Coraor 13 Feb '19

13 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0e7966e82ed6eed5b35e8fb5207e9b0f7165df18 https://github.com/galaxyproject/usegalaxy-playbook/commit/0e7966e82ed6eed5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M env/common/files/galaxy/dynamic_rules/bridges_select.py Log Message: ----------- 1. Fix a bug in the Bridges dynamic rule that would've prevented Trinity jobs for receiving more than the default 480GB of memory. 2. Set `RLIMIT_STACK` for Unicycler (SPAdes) jobs to 24MB (the value from br005), fixes #185. 3. Decrease Unicycler jobs to 288GB of memory.

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[galaxyproject/usegalaxy-playbook] fc30c9: Updated featurecounts to 1.6.3+galaxy2
by Dave B. 13 Feb '19

13 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fc30c998ead3245e883d7093c6bae15cbd9e927b https://github.com/galaxyproject/usegalaxy-playbook/commit/fc30c998ead3245e… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated featurecounts to 1.6.3+galaxy2

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