Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2829cab105c202a49904d65d88a9ac37dc12d81e https://github.com/galaxyproject/galaxy/commit/2829cab105c202a49904d65d88a9a... Author: Greg Von Kuster ghv2@psu.edu Date: 2015-11-30 (Mon, 30 Nov 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: 492fcdab9fa1cdc1465c191289077e103d8d8020 https://github.com/galaxyproject/galaxy/commit/492fcdab9fa1cdc1465c191289077... Author: Martin Cech cech.marten@gmail.com Date: 2015-11-30 (Mon, 30 Nov 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 #1193 from mvdbeek/gvk_ts_fixes

Add enhancements to the Galaxy repository install process

Compare: https://github.com/galaxyproject/galaxy/compare/f35bd9ae02aa...492fcdab9fa1