September 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] dc9378: Mutable configs
by GitHub 18 Sep '17

18 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dc937857d6d8b64cff4b801eaaeaf331baaedd24 https://github.com/galaxyproject/usegalaxy-playbook/commit/dc937857d6d8b64c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Mutable configs

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[galaxyproject/usegalaxy-playbook] ce7349: Downtime message for Main
by GitHub 18 Sep '17

18 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ce7349c409580d6a59eee9e3d2135ac95d2f1537 https://github.com/galaxyproject/usegalaxy-playbook/commit/ce7349c409580d6a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Downtime message for Main

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[galaxyproject/galaxy] 5f635b: remove .git and .hg from recursive file search
by GitHub 18 Sep '17

18 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f635bda100d7d8f93564c442c5f2d354ae453d0 https://github.com/galaxyproject/galaxy/commit/5f635bda100d7d8f93564c442c5f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-17 (Sun, 17 Sep 2017) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- remove .git and .hg from recursive file search Commit: cfb0d06575dc7523a8f7496e930b6c530e341a5c https://github.com/galaxyproject/galaxy/commit/cfb0d06575dc7523a8f7496e930b… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Exclude venv Commit: d9a805536840f9e606caee9abc0f4e2a64ffe8ea https://github.com/galaxyproject/galaxy/commit/d9a805536840f9e606caee9abc0f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/tools/loader_directory.py Log Message: ----------- Merge pull request #4636 from bgruening/find_file remove .git and .hg from recursive file search Compare: https://github.com/galaxyproject/galaxy/compare/ef602e1d1a1e...d9a805536840

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[galaxyproject/galaxy] 2c77d3: Write out registry once per job
by GitHub 18 Sep '17

18 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2c77d386def0dc21b8aa40d5d7cf5f8934c16a74 https://github.com/galaxyproject/galaxy/commit/2c77d386def0dc21b8aa40d5d7cf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Write out registry once per job Commit: e03ee53f3c398fe429ba1fe8693782a06b20cd73 https://github.com/galaxyproject/galaxy/commit/e03ee53f3c398fe429ba1fe86937… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Remove references to integrated_datatypes_config Commit: 03d9a9c6fba0e26fae080a7ebb65fd6f0676477e https://github.com/galaxyproject/galaxy/commit/03d9a9c6fba0e26fae080a7ebb65… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #4633 from mvdbeek/backport_registry_to_working_dir [17.05] Backport #4600: Write datatypes registry xml to working directory Commit: ef602e1d1a1e2b4f90d4d4ac58fb6968424b5bf6 https://github.com/galaxyproject/galaxy/commit/ef602e1d1a1e2b4f90d4d4ac58fb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-18 (Mon, 18 Sep 2017) Changed paths: M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Merge branch 'release_17.05' into dev Conflicts: lib/galaxy/datatypes/registry.py lib/galaxy/jobs/__init__.py lib/galaxy/jobs/command_factory.py lib/galaxy/tools/actions/metadata.py lib/galaxy/tools/evaluation.py Compare: https://github.com/galaxyproject/galaxy/compare/8f337f692f2a...ef602e1d1a1e

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[galaxyproject/galaxy] f3c593: fix column order in Custom Builds
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3c593fc59f0c1a43ddc992feed582cc7668caee https://github.com/galaxyproject/galaxy/commit/f3c593fc59f0c1a43ddc992feed5… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- fix column order in Custom Builds Commit: 8f337f692f2aa2a5aef766bc525929c51cad7324 https://github.com/galaxyproject/galaxy/commit/8f337f692f2aa2a5aef766bc5259… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-17 (Sun, 17 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Merge pull request #4634 from anatskiy/custom_builds_fix Fix data order in Custom Builds Compare: https://github.com/galaxyproject/galaxy/compare/13881bd264eb...8f337f692f2a

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[galaxyproject/galaxy] 2c77d3: Write out registry once per job
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 2c77d386def0dc21b8aa40d5d7cf5f8934c16a74 https://github.com/galaxyproject/galaxy/commit/2c77d386def0dc21b8aa40d5d7cf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Write out registry once per job Commit: e03ee53f3c398fe429ba1fe8693782a06b20cd73 https://github.com/galaxyproject/galaxy/commit/e03ee53f3c398fe429ba1fe86937… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Remove references to integrated_datatypes_config Commit: 03d9a9c6fba0e26fae080a7ebb65fd6f0676477e https://github.com/galaxyproject/galaxy/commit/03d9a9c6fba0e26fae080a7ebb65… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #4633 from mvdbeek/backport_registry_to_working_dir [17.05] Backport #4600: Write datatypes registry xml to working directory Compare: https://github.com/galaxyproject/galaxy/compare/97e8e3618531...03d9a9c6fba0

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[galaxyproject/galaxy] ac0844: Swap sanitize whitelist form to use a post.
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac084495978a8e5b607d90cf45dfb36c853aaf79 https://github.com/galaxyproject/galaxy/commit/ac084495978a8e5b607d90cf45df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Swap sanitize whitelist form to use a post. Commit: 13881bd264eb647bff4019ebbbf52aabf134f92b https://github.com/galaxyproject/galaxy/commit/13881bd264eb647bff4019ebbbf5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Merge pull request #4625 from dannon/sanitize_whitelist_post Swap sanitize whitelist form to use a post. Compare: https://github.com/galaxyproject/galaxy/compare/4c9cc67a8f10...13881bd264eb

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[galaxyproject/galaxy] 289799: Refactored a dataset variable to hda
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2897992ab56b69164a916ec400a2ed92b9c72d20 https://github.com/galaxyproject/galaxy/commit/2897992ab56b69164a916ec400a2… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Refactored a dataset variable to hda Commit: 4c9cc67a8f107887f341b1e386b2ac994acc2ba5 https://github.com/galaxyproject/galaxy/commit/4c9cc67a8f107887f341b1e386b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4630 from VJalili/patch-4 Refactored a dataset variable to hda Compare: https://github.com/galaxyproject/galaxy/compare/6dbd47e66197...4c9cc67a8f10

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[galaxyproject/galaxy] 432d7f: Restore correct metadata path in setup_external_me...
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 432d7f44053a7c7d1fde1504e3f382edf2a539ec https://github.com/galaxyproject/galaxy/commit/432d7f44053a7c7d1fde1504e3f3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restore correct metadata path in setup_external_metdata This is a change I shouldn't have touched in https://github.com/galaxyproject/galaxy/pull/4600 Commit: 6dbd47e661971969c734a46938a06c42b85eea8f https://github.com/galaxyproject/galaxy/commit/6dbd47e661971969c734a46938a0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4632 from mvdbeek/fix_unintended_change [BUG] Restore tool provided metadata path in setup_external_metdata Compare: https://github.com/galaxyproject/galaxy/compare/22b0542d0bb7...6dbd47e66197

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[galaxyproject/galaxy] 0624a0: remove macos testing
by GitHub 16 Sep '17

16 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0624a043a73f1a16fc36621b1c61a5cf52c67ba4 https://github.com/galaxyproject/galaxy/commit/0624a043a73f1a16fc36621b1c61… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M .travis.yml Log Message: ----------- remove macos testing Commit: 22b0542d0bb7a2f88b1503b53a8950d236be0f25 https://github.com/galaxyproject/galaxy/commit/22b0542d0bb7a2f88b1503b53a89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #4631 from martenson/disable-macos-travis disable MacOS CI on travis Compare: https://github.com/galaxyproject/galaxy/compare/153dfaa68080...22b0542d0bb7

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