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

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -04:00

common_install_util.py

The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.

2014-04-09 10:11:48 -04:00

common_util.py

The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.

2014-04-09 10:11:48 -04:00

container_util.py

The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.

2014-04-09 10:11:48 -04:00

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

Handle combinations of newly defined tool dependencies and repository dependencies that are included in updates being pulled to tool shed repositories installed into Galaxy.

2014-03-26 14:58:08 -04:00

export_util.py

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -04:00

hg_util.py

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -04:00

import_util.py

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -04:00

metadata_util.py

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -04:00

readme_util.py

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -04:00

repository_dependency_util.py

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -04:00

repository_maintenance_util.py

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -04:00

review_util.py

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -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

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -04:00

tool_dependency_util.py

Add the new repository type "Repository suite definition". This new type is associated with repositories that will contain a single file named repository_dependencies.xml that defines simple repository dependency relationships to a collection of repositories that contain related Galaxy utilities. The chemicaltoolbox repository is an example.

2014-03-27 16:03:53 -04:00

tool_util.py

Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.

2014-04-10 17:11:01 -04:00

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

Fixes for handling complex repository dependency definitions in tool dependency recipes.

2014-02-26 15:09:43 -05:00