galaxy

__init__.py

Move ~/lib/galaxy/tool_shed to ~/lib/tool_shed, and move the ~/lib/galaxy/util/shed_util componets to ~/lib/tool_shed/util.

2013-02-26 15:52:51 -05:00

commit_util.py

Fix for populating and unpopulating complex repository dependency tags sets in tool dependency definitions contained in tool shed repositories.

2013-11-19 08:52:20 -05:00

common_install_util.py

Tweak changeset 5b8c91e4183664c90f4d95699ab971e674ffd67d which created symlinks to a required tool dep endncy env.sh file for dependent tool dependencies being installed. This approach was better than the previous approach which parsed the requried repository's tool_dependencies.xml file to create the env.sh file. This changeset uses a slightly different approach: it creates an env.sh file for the dependent tool dependency whose first line "sources" the required tool dende pendcy's env.sh file. This allows for the dependent env.sh file to be managed by its tool dependency (e.g., its tool dependency may require additional env.sh paths beyond those contained in the requyired tool dependency's env.sh file). This changeset also handles sysncing the database with the file system when tool dependencies are being installed when handling a complex repository dependency definition. This process used to be handled only when not dealing with a complex repository dependency definition. This fix should correct problems encounted by the Tool Shed's install and test framework which were introduced in 5b8c91e4183664c90f4d95699ab971e674ffd67d.

2013-12-02 20:36:59 -05:00

common_util.py

Additional framework support for tool dependencies that define binary installation recipes. This change set also includes several fixes, including fixes for discovering and displaying installed and missing tool dependencies when installing a repository, fixes for the remaining issue that resulted in the creation of a so-called "white ghost" when reinstalling a repository that defines certain dependencies.

2013-09-20 11:05:30 -04:00

container_util.py

Final fixes for rendering installation errors in the tool test results container in the tool shed.

2013-12-04 10:29:59 -05:00

data_manager_util.py

Strip trailing whitespace (and windows line endings) from all python files in lib

2013-08-29 23:39:52 -04:00

datatype_util.py

Strip trailing whitespace (and windows line endings) from all python files in lib

2013-08-29 23:39:52 -04:00

encoding_util.py

Enhance the Galaxy tool migration framework to support restricted repository dependency definitions. Repository dependency definitions contained in repositories that contain tools migrated from the Galaxy code base cannot define a dependency to a repository that contains a tool at any level of the dependency hierarchy.

2013-08-26 09:57:18 -04:00

export_util.py

Improved temporary directory management in the Tool Shed.

2013-11-13 16:17:33 -05:00

import_util.py

Fix for importing repositories.

2013-11-25 13:01:44 -05:00

metadata_util.py

Fix metadata_util.py for recent changes to representation of ToolTestBuilder.inputs.

2013-11-22 10:36:01 -06:00

readme_util.py

Override the default Galaxy style for unordered lists in the Tool Shed so bullets points will display, and enhance tool config and readme file image declarations to allow for image files to be contained in a repository directory named something starting with the string 'http'.

2013-10-04 14:51:42 -04:00

repository_dependency_util.py

Code cleanup for defining and building repository dependency relationships when installing tool shed repositories into Galaxy and fixes for handling Galaxy tool panel section selection when installing repository dependencies.

2013-10-09 13:33:31 -04:00

repository_maintenance_util.py

Add the ability to import a repository capsule that was exported from a tool shed into another tool

2013-11-08 14:54:21 -05:00

review_util.py

Fix for rendering readme files in a repository that are no longer available on the file system since they are contained in an installable revision that is not the latest one in the changelog.

2013-09-24 17:09:14 -04:00

search_util.py

A bit of refactoring of the tool shed's repository controller.

2013-07-25 11:01:18 -04:00

shed_util_common.py

Fix type in my last commit - thanks John!

2013-12-02 21:35:00 -05:00

tool_dependency_util.py

Tweak changeset 5b8c91e4183664c90f4d95699ab971e674ffd67d which created symlinks to a required tool dep endncy env.sh file for dependent tool dependencies being installed. This approach was better than the previous approach which parsed the requried repository's tool_dependencies.xml file to create the env.sh file. This changeset uses a slightly different approach: it creates an env.sh file for the dependent tool dependency whose first line "sources" the required tool dende pendcy's env.sh file. This allows for the dependent env.sh file to be managed by its tool dependency (e.g., its tool dependency may require additional env.sh paths beyond those contained in the requyired tool dependency's env.sh file). This changeset also handles sysncing the database with the file system when tool dependencies are being installed when handling a complex repository dependency definition. This process used to be handled only when not dealing with a complex repository dependency definition. This fix should correct problems encounted by the Tool Shed's install and test framework which were introduced in 5b8c91e4183664c90f4d95699ab971e674ffd67d.

2013-12-02 20:36:59 -05:00

tool_util.py

Revert API tool installation fix because it break the GUI installs; API will still need a fix

2013-11-25 18:06:21 -05:00

workflow_util.py

The tool shed does not have HDAs, so step annotations cannot be displayed in a workflow in the tool shed.

2013-09-27 16:46:54 -04:00

xml_util.py

Strip trailing whitespace (and windows line endings) from all python files in lib

2013-08-29 23:39:52 -04:00