Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 31f174a4254e5cc4c85747a76c3908b0170cf358 https://github.com/galaxyproject/galaxy/commit/31f174a4254e5cc4c85747a76c390... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add enhancements to the Galaxy repository install process to cleanly handle the case described here: https://github.com/galaxyproject/galaxy/issues/667. Specifically, the following scenario is now cleanly handled: Example use case: In a toolshed I have a repository of a tool, say package_new_gene_db_1_2_3, and in revision 1 it depends on package_sqlite_1_0_0: package_new_gene_db_1_2_3 package_sqlite_1_0_0 At some point in time I discover that postgres is a better solution for my gene database, and I upload revision 2: package_new_gene_db_1_2_3 package_postgres__2_0_0 And I remove the dependecy of sqlite. If I go to my galaxy instance and I remove revision 1 and install revision 2, the installation is cleanly handled with theis PR. It should be noted that this enhancement could adversely impact reproducibility if best practices are not followed with regard to defining package dependencies. Since it is now cleanly possible to eliminate dependencies over time, best practices must be followed to ensure that elimination of a dependency does not affect the output of a tool that uses the underlying hierarchy of packages. Commit: a23e644a9cd7ab64f0fa56314ae5ec2b5a768f7a https://github.com/galaxyproject/galaxy/commit/a23e644a9cd7ab64f0fa56314ae5e... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1329 from martenson/release_15.10 [15.10] Add enhancements to the Galaxy repository install process Compare: https://github.com/galaxyproject/galaxy/compare/c48965ffcc5d...a23e644a9cd7