Commits

Author Commit Message Labels Comments Date
jeremy goecks
Set Cufflinks global model when upper quartile normalization is used.
jeremy goecks
Trackster: when running tools, replace track with group.
jeremy goecks
Trackster: use integer for dummy filter value rather than string because it is easier for client to decode.
jeremy goecks
Trackster: add support for including a global model when running tools in Trackster. This is done by using a new HiddenDataToolParameter and implementing 'set parameter' actions in a tool's trackster configuration. Cufflinks now uses a global model to produce correct output when run in Trackster.
clements
Updated "Example" images shown at the bottom of many "Operate on Genomic Invervals" tool pages. Old onew were looking dated. New ones look, well, newer, and cover more cases.
Daniel Blankenberg
Add UCSC VCF external display application.
Greg Von Kuster
Don't allow repository names to be changed if the repository has been cloned at least 1 time.
Greg Von Kuster
Make the tool_shed_install.xml.sample file ready for installing the correct versions of the emboss_5 and emboss_datatypes repositories from the main Galaxy tool shed.
Greg Von Kuster
Ensure that the integrated datatypes registry configs exist when needed.
jeremy goecks
Clean up implementation in 303741fda0ec
jeremy goecks
Add hidden attribute to tool outputs so that an output can be hidden by default.
Greg Von Kuster
Only persist the datatypes registry when the load_datatypes() method is called. Tools and metadata setting processes that create their own datatypes registry will use the existing temporary file rather than persisting the registry themselves.
Greg Von Kuster
Always set / return the absolute path of the file to which the datatypes registry is persisted.
Greg Von Kuster
Send the persisted data types registry instead of None as the value of the datatypes_config parameter to the setup_external_metadata method when creating the cmd_line in the SetMetadataToolAction.execute() method. This eliminates the use of the hard-coded 'datatypes_conf.xml' file name when setting metadata externally.
jeremy goecks
Trackster: fix bug in 13ba6909faae that prevented display in Dense mode.
Greg Von Kuster
Always attempt to remove previously written temporary xml files when persisting the current datatypes registry.
Greg Von Kuster
Enhance the datatypes registry so that it can be persisted as an xml file, which is then used for all tools instead of the datatypes config file.
Daniel Blankenberg
Add Picard Interval List to BED6 converter.
Daniel Blankenberg
Add Maximal Information-based Nonparametric Exploration (MINE) tool.
Greg Von Kuster
1) Add a new InstalledRepositoryManager class which currently enables loading datatypes from previously installed tool shed repositories into the datatypes registry. This component will enable additional features in the future. 2) Enhance the Iinstall_repository method in the admin_toolshed controller to skip displaying the page for selecting a tool panel section if no tools exist in any of the repositories being installed. 3) Eliminate duplicate generate_datatypes_metadata generate_tool_metadata generate_workflow_metadata methods and use those now contained in shed_util.py. 4) Fixes for handling tool shed repository m…
Greg Von Kuster
Enhance the datatypes registry to: (a) enable use of config files that do not include a "sniffers" tag set section, (b) not load a datatypes if the registry already includes a datatype with that extension.
jeremy goecks
Custom builds: (a) reinstitute support for len files/len entries and (b) improve UI so that it is easy to specify build definition and help is accurate.
Greg Von Kuster
Reset repository metadata for installed tool shed repositories when a new update to the repository contents has been pulled from the tool shed.
jeremy goecks
Trackster: make FeatureTracks compatible with 09c6c980e463 in preparation for enabling FeatureTracks in composite tracks.
jeremy goecks
Trackster: small fixes so that ReferenceTracks are compatible with changes in 09c6c980e463
Greg Von Kuster
1. Add a new UpdateManager for use with tool shed repositories installed into a local Galaxy instance. The UpdateManager will poll all appropriate tool sheds to see if updates are available for each of the installed repositories. Polling occurs when the Galaxy server is started. In addition, a config setting tells the UpdateManager to poll after the configured number of hours have passed. If updates are available for an installed repository, a table column is updated, and the repository name is highlighted in red, alerting the Galaxy admin that updates are available for that repository. 2. Add a new ToolIdGuidMap grid that displays all of the mappings between tool ids whose tools used to be in the distribution and guids, which is the new tool id for tools that are installed with repositories from tool sheds. 3. Add a new column named installed_changeset_revsion to the tool_shed_repository table. This column is set when the repository is installed and remains static thereafter. …
Daniel Blankenberg
Update EBI SRA tool's input action.
Dannon Baker
Provide default for robots.txt being pulled from config.
Dannon Baker
Fix default static wrapping to work with favicon.ico and robots.txt (and other static files that may need to be mapped to / in the future)
Daniel Blankenberg
Add EBI ENA SRA tool contributed by Iain Cleland.
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