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

[galaxyproject/usegalaxy-playbook] 0e7812: Update Test
by GitHub 29 Aug '17

29 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0e78126edb671cf27de4f1f6c098f578870d1e0d https://github.com/galaxyproject/usegalaxy-playbook/commit/0e78126edb671cf2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: ac6645a8edf5a0903ed7b5e65d55a32fee263961 https://github.com/galaxyproject/usegalaxy-playbook/commit/ac6645a8edf5a090… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run unicycler on bridges (Forgot to commit this when it was actually done) Commit: 234608edacbed51473b34a8418b79ec20b4e7a44 https://github.com/galaxyproject/usegalaxy-playbook/commit/234608edacbed514… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml 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: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/6db4d2f31a05...…

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[galaxyproject/usegalaxy-playbook] 6db4d2: Update Galaxy on non-CVMFS Pulsar servers when upd...
by GitHub 29 Aug '17

29 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6db4d2f31a05891846f26dfa3f67de22d7d3efa0 https://github.com/galaxyproject/usegalaxy-playbook/commit/6db4d2f31a058918… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M env/common/update.yml Log Message: ----------- Update Galaxy on non-CVMFS Pulsar servers when updating Galaxy

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[galaxyproject/galaxy] 2ede34: Fix bad merge of security patch from 17.05 into de...
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ede34659b688089ed549ea24416f7610be0a698 https://github.com/galaxyproject/galaxy/commit/2ede34659b688089ed549ea24416… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix bad merge of security patch from 17.05 into dev. Commit: d56fcf6777d93c83db5ebbc4af7968cb9889e524 https://github.com/galaxyproject/galaxy/commit/d56fcf6777d93c83db5ebbc4af79… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #4508 from jmchilton/dev_merge_fix Fix bad merge of security patch from 17.05 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/15b1a41df839...d56fcf6777d9

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[galaxyproject/galaxy] ce7d8a: Validate workflow step after step argument injecti...
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce7d8a2fc1bcc1f9241028b3d437c653edccda0c https://github.com/galaxyproject/galaxy/commit/ce7d8a2fc1bcc1f9241028b3d437… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Validate workflow step after step argument injection Commit: 3ef39b390c8d2f66ff890a29b712f785b6376601 https://github.com/galaxyproject/galaxy/commit/3ef39b390c8d2f66ff890a29b712… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js Log Message: ----------- Fix drag and drop from history for firefox Commit: cf897795fe8b544bc4cb5899585b1be2ee0063e6 https://github.com/galaxyproject/galaxy/commit/cf897795fe8b544bc4cb5899585b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js Log Message: ----------- Merge pull request #4496 from guerler/fix_drag_drop_firefox [17.05] Fix drag and drop from history for Firefox Commit: c70926445fb7518e1f2ebf755477ca3327dea6a3 https://github.com/galaxyproject/galaxy/commit/c70926445fb7518e1f2ebf755477… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4483 from guerler/fix_workflow_validation [17.05] Validate workflow step after step argument injection Commit: 1d485390b0af80441c4e577f8fb7ddde265f9618 https://github.com/galaxyproject/galaxy/commit/1d485390b0af80441c4e577f8fb7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 9337c9fdc118f7c4883a6c7b4cada483b09461c7 https://github.com/galaxyproject/galaxy/commit/9337c9fdc118f7c4883a6c7b4cad… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/datatypes/data.py M lib/galaxy/workflow/modules.py M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js Log Message: ----------- Merge branch 'release_17.05' into merge-release1705 Commit: 8aefa9d49535b7592bd7398541f9cbeaba9146ce https://github.com/galaxyproject/galaxy/commit/8aefa9d49535b7592bd7398541f9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js Log Message: ----------- repack client Commit: 15b1a41df83940961d8f516e4023cd410b38964b https://github.com/galaxyproject/galaxy/commit/15b1a41df83940961d8f516e4023… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/datatypes/data.py M lib/galaxy/workflow/modules.py M static/maps/mvc/ui/ui-select-content.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/ui/ui-select-content.js Log Message: ----------- Merge pull request #4506 from martenson/merge-release1705 Merge release_17.05 to dev Compare: https://github.com/galaxyproject/galaxy/compare/f159df391ea4...15b1a41df839

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[galaxyproject/galaxy] e61553: 2017-08 Security Patch
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e6155367e61d8b4e66883992db6af88444f346a0 https://github.com/galaxyproject/galaxy/commit/e6155367e61d8b4e66883992db6a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: f159df391ea4eeaac01779426cfad00e38b5f907 https://github.com/galaxyproject/galaxy/commit/f159df391ea4eeaac01779426cfa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- Merge pull request #4501 from erasche/2017-08-security 2017-08 Security Patch Compare: https://github.com/galaxyproject/galaxy/compare/4b9b14979a71...f159df391ea4

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[galaxyproject/galaxy] 2ff429: move to somewhere it can be overridden
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ff4292cd6171fc128e91ddbb66f5124368c25ee https://github.com/galaxyproject/galaxy/commit/2ff4292cd6171fc128e91ddbb66f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- move to somewhere it can be overridden Commit: 68f9c6905ef56ce9b82e2889a48b4185370e83b4 https://github.com/galaxyproject/galaxy/commit/68f9c6905ef56ce9b82e2889a48b… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less Log Message: ----------- Large click target for tools Commit: cd6cc88ac19b5d7c218e31fb14c74382d2439a1f https://github.com/galaxyproject/galaxy/commit/cd6cc88ac19b5d7c218e31fb14c7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/style/less/galaxy_variables.less A client/galaxy/style/less/theme/plain.less M static/maps/mvc/tool/tools.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/tool/tools.js Log Message: ----------- Plain theme Commit: 97ee0f1fcdd7d059d5c37e1bb25a8c3389559698 https://github.com/galaxyproject/galaxy/commit/97ee0f1fcdd7d059d5c37e1bb25a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M static/style/blue/base.css Log Message: ----------- rebuild style Commit: 4b9b14979a7137f4aca90e1e1e7869e88ae1bb6e https://github.com/galaxyproject/galaxy/commit/4b9b14979a7137f4aca90e1e1e78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/galaxy_variables.less A client/galaxy/style/less/theme/plain.less M static/maps/mvc/tool/tools.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/tool/tools.js M static/style/blue/base.css Log Message: ----------- Merge pull request #4470 from erasche/retheme Nicer tool click targets for base + "plain" theme Compare: https://github.com/galaxyproject/galaxy/compare/426aa310fd21...4b9b14979a71

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[galaxyproject/galaxy] 1d4853: 2017-08 Security Patch
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 1d485390b0af80441c4e577f8fb7ddde265f9618 https://github.com/galaxyproject/galaxy/commit/1d485390b0af80441c4e577f8fb7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch

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[galaxyproject/galaxy] 5a1846: 2017-08 Security Patch
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 5a18464d547d7497285ee25067050ee4cd665eda https://github.com/galaxyproject/galaxy/commit/5a18464d547d7497285ee2506705… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch

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[galaxyproject/galaxy] 47ba64: 2017-08 Security Patch
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 47ba644de78dd82cfaed205128bd34056aa99078 https://github.com/galaxyproject/galaxy/commit/47ba644de78dd82cfaed205128bd… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch

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[galaxyproject/galaxy] ce7d8a: Validate workflow step after step argument injecti...
by GitHub 25 Aug '17

25 Aug '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: ce7d8a2fc1bcc1f9241028b3d437c653edccda0c https://github.com/galaxyproject/galaxy/commit/ce7d8a2fc1bcc1f9241028b3d437… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Validate workflow step after step argument injection Commit: c70926445fb7518e1f2ebf755477ca3327dea6a3 https://github.com/galaxyproject/galaxy/commit/c70926445fb7518e1f2ebf755477… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4483 from guerler/fix_workflow_validation [17.05] Validate workflow step after step argument injection Compare: https://github.com/galaxyproject/galaxy/compare/cf897795fe8b...c70926445fb7

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