Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 96cf1b94f14b7c92c767943fa4595e638eb322e3
https://github.com/galaxyproject/galaxy/commit/96cf1b94f14b7c92c767943fa459…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
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/collection/list-of-pairs-collection-creator.js
Log Message:
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Lower threshold for auto-matching dataset pairs in the collection builder.
Thanks to @mvdbeek for originally testing this and verifying it works.
Fixes #4349.
Commit: a13bd06f48eb1eda43c034e3fe0a3d9363d8cda4
https://github.com/galaxyproject/galaxy/commit/a13bd06f48eb1eda43c034e3fe0a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
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/collection/list-of-pairs-collection-creator.js
Log Message:
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Merge pull request #4555 from jmchilton/lower_matching_threshold
Lower threshold for auto-matching dataset pairs in the collection builder
Compare: https://github.com/galaxyproject/galaxy/compare/1e3bd2d4e831...a13bd06f48eb
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 946d64b8f7dc08b92ebb03f34a91cab8aa7ecfbb
https://github.com/galaxyproject/galaxy/commit/946d64b8f7dc08b92ebb03f34a91…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
A lib/galaxy/tools/deps/resolvers/lmod.py
Log Message:
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LMOD Dependency resolver - Initial commit (lib lmod.py)
Initial commit of a prototype dependency resolver based on the LMOD environment modules system.
Commit: 4d143479d5998531cc4803af11579e12d160c87b
https://github.com/galaxyproject/galaxy/commit/4d143479d5998531cc4803af1157…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
Log Message:
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Update of the dependency_resolvers_conf.xml.sample file
Addition of the LMOD Dependency resolver to the appropriate sample configuration file (dependency_resolvers_conf.xml.sample). Comment lines have also been added to describe the possible attributes of the resolver as well as their default values.
Commit: e84284c477182b3c03e785b79f93dd88d63e6ebd
https://github.com/galaxyproject/galaxy/commit/e84284c477182b3c03e785b79f93…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-23 (Wed, 23 Aug 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
A config/lmod_modules_mapping.yml.sample
M lib/galaxy/tools/deps/resolvers/lmod.py
Log Message:
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LMOD Dependency resolver - Default mapping file
If a lmod_modules_mapping.yml file exists in the config folder then it will be taken into consideration automatically to map Galaxy requirements to LMOD modules.
Commit: fed3206a87e4ae4ede380c90cfa3409220847cf7
https://github.com/galaxyproject/galaxy/commit/fed3206a87e4ae4ede380c90cfa3…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/lmod.py
Log Message:
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Fix errors reported by the initial Travis tests
Fix incorrect numbers of blank lines.
Fix deprecated syntax.
Commit: 09887529765ba88adb70e739d1b9d8896cb86229
https://github.com/galaxyproject/galaxy/commit/09887529765ba88adb70e739d1b9…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/lmod.py
Log Message:
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Syntax fix in the shell_commands method
The built command now reflect more directly the command that is really executed by the the LMOD "module" bash function when a user execute "module load package_name/package_version".
Commit: 574e697a4d66a53f298f37f4987d31db96ff8e14
https://github.com/galaxyproject/galaxy/commit/574e697a4d66a53f298f37f4987d…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
Log Message:
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Dependency_resolvers_conf.xml - More explanations
Some more explanations about the versionless mode have been added.
Commit: db5efdaa7cbc197eaf6a777d4d390de24b212e88
https://github.com/galaxyproject/galaxy/commit/db5efdaa7cbc197eaf6a777d4d39…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/lmod.py
Log Message:
-----------
Clearer comment lines in the has_module method
A comment of the has_module method of the AvailModuleChecker class has been modified to be clearer and more explicit.
Commit: eda36ffb99a1abec8f878c0b7ae194938781c8d6
https://github.com/galaxyproject/galaxy/commit/eda36ffb99a1abec8f878c0b7ae1…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M test/unit/tools/test_tool_deps.py
Log Message:
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LMOD Dependency resolver - Unit tests added
The unit/tools/tests_tool_deps.py script has been updated to includ unit tests for the LMOD dependency resolver.
Commit: bbec357bbd744b9e0d760e8d0903adfa43d1b7e2
https://github.com/galaxyproject/galaxy/commit/bbec357bbd744b9e0d760e8d0903…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M test/unit/tools/test_tool_deps.py
Log Message:
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Fix the import order error raised by Travis
The order of the import statements in the test_tool_deps script was incorrect (as stated by travis). That should no longer be the case.
Commit: 9822f5f2a91fae7e3420a06c58f2621a2cf084ac
https://github.com/galaxyproject/galaxy/commit/9822f5f2a91fae7e3420a06c58f2…
Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M test/unit/tools/test_tool_deps.py
Log Message:
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Fix attempt for the modulepath issue in unit tests
On a computer where LMOD is not installed, the MODULEPATH variable is not defined and the modulepath attributes of the LMOD dependency resolver must be used.
Commit: 1e3bd2d4e831331b8e3b314bac287288fa4533fc
https://github.com/galaxyproject/galaxy/commit/1e3bd2d4e831331b8e3b314bac28…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-05 (Tue, 05 Sep 2017)
Changed paths:
M config/dependency_resolvers_conf.xml.sample
A config/lmod_modules_mapping.yml.sample
A lib/galaxy/tools/deps/resolvers/lmod.py
M test/unit/tools/test_tool_deps.py
Log Message:
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Merge pull request #4489 from arbernard/LMOD_Dependency_resolver
New Dependency resolver for the LMOD environment modules system
Compare: https://github.com/galaxyproject/galaxy/compare/6e6845b4987a...1e3bd2d4e831