November 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] d5132a: Log invalid xml filename
by GitHub 04 Nov '16

04 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5132a374c25d17e63a19379bcec1d42b99f8547 https://github.com/galaxyproject/galaxy/commit/d5132a374c25d17e63a19379bcec… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: 37399049552dd1f2f4492e4eb9f168ac8a9abd5f https://github.com/galaxyproject/galaxy/commit/37399049552dd1f2f4492e4eb9f1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3124 from mvdbeek/escape_sections Log invalid xml filename Compare: https://github.com/galaxyproject/galaxy/compare/4866e72ad22b...37399049552d

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[galaxyproject/galaxy] 5e19d6: Escape section id and name when writing integrated...
by GitHub 04 Nov '16

04 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5e19d6c57465ce79d4ee96e3206542ac655d137d https://github.com/galaxyproject/galaxy/commit/5e19d6c57465ce79d4ee96e32065… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: 4866e72ad22b1772f93c8973e51f32086896277f https://github.com/galaxyproject/galaxy/commit/4866e72ad22b1772f93c8973e51f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Merge pull request #3122 from mvdbeek/escape_sections Escape section name when writing to xml, Compare: https://github.com/galaxyproject/galaxy/compare/1d8f31c4f488...4866e72ad22b

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[galaxyproject/usegalaxy-playbook] 4150f1: Increase flanking_features_1 to 16GB
by GitHub 03 Nov '16

03 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4150f10af479199882735a039af2769edb4e9a9d https://github.com/galaxyproject/usegalaxy-playbook/commit/4150f10af4791998… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase flanking_features_1 to 16GB

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[galaxyproject/galaxy] 6082f7: Fix path
by GitHub 03 Nov '16

03 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6082f790438d6fc04f313c2eef273bfa43ff0715 https://github.com/galaxyproject/galaxy/commit/6082f790438d6fc04f313c2eef27… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Fix path Broken in #2131. Reported by @dnbenso at https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1… Commit: 65338b3adb925f27142c6fdf45af7f8d01e57f9d https://github.com/galaxyproject/galaxy/commit/65338b3adb925f27142c6fdf45af… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #3112 from nsoranzo/release_16.04_fix_for_2131 [16.04] Fix path in run_tool_shed.sh Commit: d72cc77bebd46b0e60d09e19cee2496777503f11 https://github.com/galaxyproject/galaxy/commit/d72cc77bebd46b0e60d09e19cee2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 1d8f31c4f488dc380ffe657e5fa4a9d9cdd697ae https://github.com/galaxyproject/galaxy/commit/1d8f31c4f488dc380ffe657e5fa4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/94fd3a51a2a3...1d8f31c4f488

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[galaxyproject/galaxy] 6082f7: Fix path
by GitHub 03 Nov '16

03 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 6082f790438d6fc04f313c2eef273bfa43ff0715 https://github.com/galaxyproject/galaxy/commit/6082f790438d6fc04f313c2eef27… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Fix path Broken in #2131. Reported by @dnbenso at https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1… Commit: 65338b3adb925f27142c6fdf45af7f8d01e57f9d https://github.com/galaxyproject/galaxy/commit/65338b3adb925f27142c6fdf45af… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #3112 from nsoranzo/release_16.04_fix_for_2131 [16.04] Fix path in run_tool_shed.sh Commit: d72cc77bebd46b0e60d09e19cee2496777503f11 https://github.com/galaxyproject/galaxy/commit/d72cc77bebd46b0e60d09e19cee2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/5963a2fa22e6...d72cc77bebd4

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[galaxyproject/galaxy] 6082f7: Fix path
by GitHub 03 Nov '16

03 Nov '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 6082f790438d6fc04f313c2eef273bfa43ff0715 https://github.com/galaxyproject/galaxy/commit/6082f790438d6fc04f313c2eef27… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Fix path Broken in #2131. Reported by @dnbenso at https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1… Commit: 65338b3adb925f27142c6fdf45af7f8d01e57f9d https://github.com/galaxyproject/galaxy/commit/65338b3adb925f27142c6fdf45af… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M run_tool_shed.sh Log Message: ----------- Merge pull request #3112 from nsoranzo/release_16.04_fix_for_2131 [16.04] Fix path in run_tool_shed.sh Compare: https://github.com/galaxyproject/galaxy/compare/2adb98e58cc0...65338b3adb92

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[galaxyproject/galaxy] 8f89a0: Fix job_working_directory commented default
by GitHub 03 Nov '16

03 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8f89a04eae27e615434e268f93d492b6c0cd54be https://github.com/galaxyproject/galaxy/commit/8f89a04eae27e615434e268f93d4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix job_working_directory commented default Follow-up to commit 0eab8346b3dd3ee7788c9cdda0f10f8aea4b2726. Commit: 83760e6a01cd3fa16a17158bb1182ffebb00c5d7 https://github.com/galaxyproject/galaxy/commit/83760e6a01cd3fa16a17158bb118… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M doc/source/conf.py Log Message: ----------- Don't skip __init__() methods when generating docs Commit: 402f2815c23d695f0673d0af9acb9cf0e3527afa https://github.com/galaxyproject/galaxy/commit/402f2815c23d695f0673d0af9acb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Drop code which is never executed After commit 59583f26ea11b44cb17f260230be820b304cd918, self.object_store_config_file is always set. Commit: ad515397388056b8587c80350b755444602a49d0 https://github.com/galaxyproject/galaxy/commit/ad515397388056b8587c80350b75… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Fix typo Commit: 0c28a64269048ea21701e6c5b358d783bdde8eed https://github.com/galaxyproject/galaxy/commit/0c28a64269048ea21701e6c5b358… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/objectstore/rods.py Log Message: ----------- Remove redundant ObjectStore superclass Commit: 1c68e0af3e9a02250d0d12c2149dcdbb1caf2da2 https://github.com/galaxyproject/galaxy/commit/1c68e0af3e9a02250d0d12c2149d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Fix object stores' __init__() methods doc Also: - remove unused parameters when calling the parent constructors - Python3 compatibility Commit: 94fd3a51a2a3a46aa4a834ed6d7d0bb50e6154a5 https://github.com/galaxyproject/galaxy/commit/94fd3a51a2a3a46aa4a834ed6d7d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M config/galaxy.ini.sample M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py Log Message: ----------- Merge pull request #3119 from nsoranzo/misc_fixes Object store and other misc fixes Compare: https://github.com/galaxyproject/galaxy/compare/aa72f4a0b62a...94fd3a51a2a3

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[galaxyproject/galaxy]
by GitHub 02 Nov '16

02 Nov '16

Branch: refs/heads/tool_tarball_fix Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 892237: Fix linting broken in #3080
by GitHub 02 Nov '16

02 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 892237bf0042e458db7c7220eb4faf022b5a7650 https://github.com/galaxyproject/galaxy/commit/892237bf0042e458db7c7220eb4f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix linting broken in #3080 Also fix import order and Python3 compatibility. Commit: aa72f4a0b62a7795bc726dd75bdb7635d29afef5 https://github.com/galaxyproject/galaxy/commit/aa72f4a0b62a7795bc726dd75bdb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #3116 from nsoranzo/fix_for_3080 Fix linting broken in #3080 Compare: https://github.com/galaxyproject/galaxy/compare/ef3e63e6d732...aa72f4a0b62a

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[galaxyproject/galaxy] 600112: remove the communication server check
by GitHub 02 Nov '16

02 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 600112256970c1024b3ba4e6fa57cd61f9fe199d https://github.com/galaxyproject/galaxy/commit/600112256970c1024b3ba4e6fa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- remove the communication server check from non-galaxy calls Commit: cf0e4e84ce4137334ee6e8c20e56a52070179c4d https://github.com/galaxyproject/galaxy/commit/cf0e4e84ce4137334ee6e8c20e56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-14 (Fri, 14 Oct 2016) Changed paths: M templates/user/index.mako Log Message: ----------- Merge pull request #3053 from martenson/fix-userindex-for-ts [16.07] remove the communication server check Commit: 096a7bf94d799f905013f7052c1bdf87062a45a7 https://github.com/galaxyproject/galaxy/commit/096a7bf94d799f905013f7052c1b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.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/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the incorrect handling of root when prefix is in play Commit: 65dc4f22aa7b717109aca6fac7947a84d2bd587a https://github.com/galaxyproject/galaxy/commit/65dc4f22aa7b717109aca6fac794… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-23 (Sun, 23 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.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/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #3074 from martenson/fix-libraries-prefix [16.07] Fix libraries prefix Commit: 9abe863f26ba742c9f362b3a8177af5c8efa5741 https://github.com/galaxyproject/galaxy/commit/9abe863f26ba742c9f362b3a8177… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix loading of collection operations If MODEL_TOOLS_PATH is not absolute, it will be joined with tool_path (i.e. './tools' ) inside _load_tool_tag_set(), so Galaxy will try to load e.g. './tools/lib/galaxy/tools/unzip_collection.xml' Commit: 5963a2fa22e64b5494a1aa00931808a11d792cbd https://github.com/galaxyproject/galaxy/commit/5963a2fa22e64b5494a1aa009318… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3115 from nsoranzo/release_16.07_fix_collection_ops_loading [16.07] Fix loading of collection operations Commit: ef3e63e6d7327719a4581bb939dff8fd1ac1fcd9 https://github.com/galaxyproject/galaxy/commit/ef3e63e6d7327719a4581bb939df… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.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/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M templates/user/index.mako Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: static/scripts/bundled/analysis.bundled.js 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/38dd9ca509ed...ef3e63e6d732

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