galaxy-commits December 2016

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[galaxyproject/galaxy] 86447e: Add support for ESTScan scores matrices (smat) dat...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 86447eced8eb1d0966253a15e3f889bfc97dad17 https://github.com/galaxyproject/galaxy/commit/86447eced8eb1d0966253a15e3f8… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2016-12-02 (Fri, 02 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/test/1.smat M lib/galaxy/datatypes/text.py Log Message: ----------- Add support for ESTScan scores matrices (smat) data type Commit: e08e7827e5df961554e05a0c87eaa7359659c2c3 https://github.com/galaxyproject/galaxy/commit/e08e7827e5df961554e05a0c87ea… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Eliminate unnecessary file close Commit: 147de088177c262c9ad3fd13ac4929217bee6618 https://github.com/galaxyproject/galaxy/commit/147de088177c262c9ad3fd13ac49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/test/1.smat M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #3258 from gregvonkuster/smat2 Add support for ESTScan scores matrices (smat) data type Compare: https://github.com/galaxyproject/galaxy/compare/553f781d3921...147de088177c

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[galaxyproject/galaxy] d61356: changed ipython to jupyter
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d61356dfeaaa4e2e7f0b0a58875a90da67aa210c https://github.com/galaxyproject/galaxy/commit/d61356dfeaaa4e2e7f0b0a58875a… Author: Anne Fouilloux <annefou(a)uio.no> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/datatypes/text.py Log Message: ----------- changed ipython to jupyter When converting jupyter notebook to html, ipython command is used instead of jupyter (ipython is becoming obsolete). Commit: 93da60c48e9947b2ae5f7ff080db20fbcd59c51f https://github.com/galaxyproject/galaxy/commit/93da60c48e9947b2ae5f7ff080db… Author: Anne Fouilloux <annefou(a)uio.no> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/dev/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/datatypes/text.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/proxy/js/Dockerfile M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Changed ipython with jupyter not only for converting jupyter notebook to HTML (with nbconvert) but also where ipython/IPython was referenced. Some files still contain ipython but this is mostly related to documentation or to the IE docker container itself. Commit: 7468ea3d34312b1562454d43a2eaf0158ac5478e https://github.com/galaxyproject/galaxy/commit/7468ea3d34312b1562454d43a2ea… Author: Anne Fouilloux <annefou(a)uio.no> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M doc/Makefile A doc/fix_schema_rst.sh M doc/source/admin/index.rst M doc/source/admin/webhooks.rst M doc/source/project/organization.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/deps/installable.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev to take into account the latest changes done on the galaxyproject Commit: 553f781d39218d9b717e5a09ebfcf5214e680e16 https://github.com/galaxyproject/galaxy/commit/553f781d39218d9b717e5a09ebfc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/dev/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/datatypes/text.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/proxy/js/Dockerfile M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge pull request #3294 from annefou/dev changed ipython to jupyter Compare: https://github.com/galaxyproject/galaxy/compare/330cb432e819...553f781d3921

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[galaxyproject/galaxy] b4c4d9: fixed a typo
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4c4d9836cbfc77230dd156e4ff701040b8c08f7 https://github.com/galaxyproject/galaxy/commit/b4c4d9836cbfc77230dd156e4ff7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- fixed a typo Commit: 330cb432e819ebb2e8f28bf99a6aad3d5b70c863 https://github.com/galaxyproject/galaxy/commit/330cb432e819ebb2e8f28bf99a6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3322 from anatskiy/hotfix/run_tests_typo run_tests.sh: a small typo Compare: https://github.com/galaxyproject/galaxy/compare/36895d1dce26...330cb432e819

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[galaxyproject/infrastructure-playbook] c5e03a: Redirect getgalaxy.org to from wiki to new site.
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c5e03a2fa2e8aae381d7dad0e891986929514ce3 https://github.com/galaxyproject/infrastructure-playbook/commit/c5e03a2fa2e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M galaxyenv/templates/nginx/galaxydomains.j2 Log Message: ----------- Redirect getgalaxy.org to from wiki to new site.

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[galaxyproject/galaxy] c1e308: Fix an ACE vulnerability with gff filter tools. Th...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/release_14.10 Home: https://github.com/galaxyproject/galaxy Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934 https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure.

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[galaxyproject/galaxy] c1e308: Fix an ACE vulnerability with gff filter tools. Th...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/release_15.01 Home: https://github.com/galaxyproject/galaxy Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934 https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572 https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Compare: https://github.com/galaxyproject/galaxy/compare/61cd045ffa94...9ee3d01c301c

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[galaxyproject/galaxy] c1e308: Fix an ACE vulnerability with gff filter tools. Th...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/release_15.03 Home: https://github.com/galaxyproject/galaxy Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934 https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572 https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844 https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e18… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Compare: https://github.com/galaxyproject/galaxy/compare/0122040fad86...da7afb4e22f3

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[galaxyproject/galaxy] c1e308: Fix an ACE vulnerability with gff filter tools. Th...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934 https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572 https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844 https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e18… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 7c443eda567ece12fb90330e131e7f97c7b63ba2 https://github.com/galaxyproject/galaxy/commit/7c443eda567ece12fb90330e131e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Compare: https://github.com/galaxyproject/galaxy/compare/c8e9845c5c57...7c443eda567e

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[galaxyproject/galaxy] c1e308: Fix an ACE vulnerability with gff filter tools. Th...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934 https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572 https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844 https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e18… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 7c443eda567ece12fb90330e131e7f97c7b63ba2 https://github.com/galaxyproject/galaxy/commit/7c443eda567ece12fb90330e131e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 790e60af60093dcb8e26f093c3a87903605da206 https://github.com/galaxyproject/galaxy/commit/790e60af60093dcb8e26f093c3a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Compare: https://github.com/galaxyproject/galaxy/compare/30608c177c62...790e60af6009

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[galaxyproject/galaxy] c1e308: Fix an ACE vulnerability with gff filter tools. Th...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934 https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for the disclosure. Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572 https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_14.10' into release_15.01 Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844 https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e18… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 7c443eda567ece12fb90330e131e7f97c7b63ba2 https://github.com/galaxyproject/galaxy/commit/7c443eda567ece12fb90330e131e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: 790e60af60093dcb8e26f093c3a87903605da206 https://github.com/galaxyproject/galaxy/commit/790e60af60093dcb8e26f093c3a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: 95daf69b372fa829325be561dc0a9907da0bea81 https://github.com/galaxyproject/galaxy/commit/95daf69b372fa829325be561dc0a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_15.07' into release_15.10 Compare: https://github.com/galaxyproject/galaxy/compare/a2114fdd0e23...95daf69b372f

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galaxy-commits December 2016