galaxy-commits February 2016

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135 discussions

[galaxyproject/galaxy] f2a27a: Drop Python 2.6 with 16.04.
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f2a27acff8fd5d199eda841fd575305c3644c439 https://github.com/galaxyproject/galaxy/commit/f2a27acff8fd5d199eda841fd575… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- Drop Python 2.6 with 16.04. xref #1596 Commit: 805b5906b2f43947af36814fe67b5914acc35a08 https://github.com/galaxyproject/galaxy/commit/805b5906b2f43947af36814fe67b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge pull request #1772 from jmchilton/python26_drop [16.01] Deprecation notice - Python 2.6. Compare: https://github.com/galaxyproject/galaxy/compare/3621d6f22125...805b5906b2f4

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[galaxyproject/galaxy] 9acbfd: Fix chrome-only intermittent rendering error of fo...
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 9acbfdf3c3444ca0cb0cf87f80c57d00765673d9 https://github.com/galaxyproject/galaxy/commit/9acbfdf3c3444ca0cb0cf87f80c5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M static/style/blue/base.css Log Message: ----------- Fix chrome-only intermittent rendering error of font awesome icons that have their sizes changed by overriding 4.2 font-size inheritance rule from core.less Commit: 3621d6f2212566b8a172424177b8eafc92af7fca https://github.com/galaxyproject/galaxy/commit/3621d6f2212566b8a172424177b8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/ui/icon-btn.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1784 from carlfeberhard/fix.fa [16.01] Fix chrome-only intermittent rendering error of font awesome icons th… Compare: https://github.com/galaxyproject/galaxy/compare/4c815a7d0589...3621d6f22125

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[galaxyproject/galaxy] dda851: Fix sections
by GitHub 24 Feb '16

24 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dda851def5e30ea0b48bd9535a7b2f075a1af63b https://github.com/galaxyproject/galaxy/commit/dda851def5e30ea0b48bd9535a7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix sections Commit: a41f4750179c7306c176a6149e821e2a32993fcf https://github.com/galaxyproject/galaxy/commit/a41f4750179c7306c176a6149e82… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1783 from guerler/fix_sections_000 Fix tool form rendering of sections Compare: https://github.com/galaxyproject/galaxy/compare/390d3b7eb70b...a41f4750179c

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[galaxyproject/galaxy] dbab6f: Workaround for #1739 - fixing up subworkflow inut ...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dbab6f5b979f19c33c3cd1aeb5c459dcc5612eec https://github.com/galaxyproject/galaxy/commit/dbab6f5b979f19c33c3cd1aeb5c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map 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/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Workaround for #1739 - fixing up subworkflow inut connections. Do the same relaxed thing we do for inputs of type 'input' as we do for outputs of this type. Someday we should have better tracking, but such a change is probably not wise for a release branch. Commit: 5b720b4a02408a0601e7ecaf4fb2374c8c5753a7 https://github.com/galaxyproject/galaxy/commit/5b720b4a02408a0601e7ecaf4fb2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map 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/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1774 from jmchilton/wf_fixes [16.01] Workaround for #1739 - fixing up subworkflow input connections. Commit: 4c815a7d0589a00df8c8fffba730a79030ad7791 https://github.com/galaxyproject/galaxy/commit/4c815a7d0589a00df8c8fffba730… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1778 from nsoranzo/release_16.01_fix_download_file [16.01] Strip URL of download_file and download_by_url install actions. Commit: 390d3b7eb70b438d215d66180342aa86c9e1e7f1 https://github.com/galaxyproject/galaxy/commit/390d3b7eb70b438d215d66180342… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge branch 'release_16.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/f06b8205897a...390d3b7eb70b

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[galaxyproject/usegalaxy-playbook] c1f80b: Update Test and Main Tool Shed
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c1f80b83ba1e5edd4b1751b356faf5d8ee93d0a0 https://github.com/galaxyproject/usegalaxy-playbook/commit/c1f80b83ba1e5edd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M production/group_vars/toolshedservers.yml M stage/group_vars/toolshedservers.yml Log Message: ----------- Update Test and Main Tool Shed

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[galaxyproject/usegalaxy-playbook] a63287: Update Test and Main
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a63287b90a825caad36a7caa5c08a9db50304e21 https://github.com/galaxyproject/usegalaxy-playbook/commit/a63287b90a825caa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version A production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample A production/files/interactive_environments/plugins/phinch/config/phinch.xml A production/files/interactive_environments/plugins/phinch/static/js/phinch.js A production/files/interactive_environments/plugins/phinch/templates/phinch.mako M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/group_vars/all.yml M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/group_vars/all.yml M stage/inventory Log Message: ----------- Update Test and Main Commit: 55a3aea169de339b7dd380e09283613c2eddeed2 https://github.com/galaxyproject/usegalaxy-playbook/commit/55a3aea169de339b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs from Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c9696f8218c4...…

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[galaxyproject/galaxy] 5ce771: Strip URL of download_file and download_by_url ins...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 5ce771b70e44f28fde2e14bf963f97fed36bc2ae https://github.com/galaxyproject/galaxy/commit/5ce771b70e44f28fde2e14bf963f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Strip URL of download_file and download_by_url install actions. Commit: 4c815a7d0589a00df8c8fffba730a79030ad7791 https://github.com/galaxyproject/galaxy/commit/4c815a7d0589a00df8c8fffba730… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1778 from nsoranzo/release_16.01_fix_download_file [16.01] Strip URL of download_file and download_by_url install actions. Compare: https://github.com/galaxyproject/galaxy/compare/5b720b4a0240...4c815a7d0589

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[galaxyproject/galaxy] 5ce771: Strip URL of download_file and download_by_url ins...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ce771b70e44f28fde2e14bf963f97fed36bc2ae https://github.com/galaxyproject/galaxy/commit/5ce771b70e44f28fde2e14bf963f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Strip URL of download_file and download_by_url install actions. Commit: f06b8205897a594b9d10e3f0aeb37f4858ca15c6 https://github.com/galaxyproject/galaxy/commit/f06b8205897a594b9d10e3f0aeb3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1775 from nsoranzo/release_16.01_fix_download_file [16.01] Strip URL of download_file and download_by_url install actions. Compare: https://github.com/galaxyproject/galaxy/compare/4498c50f90c9...f06b8205897a

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[galaxyproject/galaxy] dbab6f: Workaround for #1739 - fixing up subworkflow inut ...
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: dbab6f5b979f19c33c3cd1aeb5c459dcc5612eec https://github.com/galaxyproject/galaxy/commit/dbab6f5b979f19c33c3cd1aeb5c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map 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/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Workaround for #1739 - fixing up subworkflow inut connections. Do the same relaxed thing we do for inputs of type 'input' as we do for outputs of this type. Someday we should have better tracking, but such a change is probably not wise for a release branch. Commit: 5b720b4a02408a0601e7ecaf4fb2374c8c5753a7 https://github.com/galaxyproject/galaxy/commit/5b720b4a02408a0601e7ecaf4fb2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map 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/mvc/workflow/workflow-terminals.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1774 from jmchilton/wf_fixes [16.01] Workaround for #1739 - fixing up subworkflow input connections. Compare: https://github.com/galaxyproject/galaxy/compare/b5e91d23779c...5b720b4a0240

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[galaxyproject/galaxy] aa27fc: better default than localhost
by GitHub 23 Feb '16

23 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa27fcf75bd8fe7bb0bcab5428ff80a6b750a41e https://github.com/galaxyproject/galaxy/commit/aa27fcf75bd8fe7bb0bcab5428ff… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-21 (Sun, 21 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- better default than localhost Commit: 5d37f9b103af0d9f4773528eabb5e4a81ceaa704 https://github.com/galaxyproject/galaxy/commit/5d37f9b103af0d9f4773528eabb5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-21 (Sun, 21 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- missing quotes Commit: bad1aca5a9fded2547e43dd66f37500d64e22655 https://github.com/galaxyproject/galaxy/commit/bad1aca5a9fded2547e43dd66f37… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Split out inspect and container_port_mapping / container_gateway_ip recovery, fix typo. Commit: e718e8ebac640109d0b1ed6f0c706705ab315d2d https://github.com/galaxyproject/galaxy/commit/e718e8ebac640109d0b1ed6f0c70… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- docstring fixes Commit: 4498c50f90c9113c793a45066b52ea4ba5b208fa https://github.com/galaxyproject/galaxy/commit/4498c50f90c9113c793a45066b52… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1770 from mvdbeek/fix_ies Use "Gateway" from docker inspect as default docker_hostname Compare: https://github.com/galaxyproject/galaxy/compare/1b25944a5d83...4498c50f90c9

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galaxy-commits February 2016