Swift Enabled Galaxy Workflows ------------------------------- This section documents running Swift enabled workflows in Galaxy environment. Galaxy is a workflow portal environment through which users can compose workflows via galaxy-tools chained together via inputs and outputs. See Galaxy home page to know more about Galaxy user environment. Writing Swift-enabled Galaxy Tool ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Following is a template to write Swift-enabled Galaxy tools. It contains a single self contained script. Following is an example Galaxy-tool generated with the above mentioned template script. It has capability to process a dataset that resides outside of Galaxy, and to create a new dataset that resides outside of Galaxy. Each dataset could be a list of one or more external references such as GridFTP URIs or authenticated GO transfers. The tool can invoke other (non-swift) Galaxy tools as app() functions within the embedded Swift script. Generic Swift Galaxy Tool ~~~~~~~~~~~~~~~~~~~~~~~~~~ A Generic Swift Galaxy Tool which allows users to add arbitrary Swift scripts, input data and designated outputs. This tool can be used as a hosted 'try-swift' capability. User can push in new Swift workflows as tools. User can set config related values using web forms: drop-downs or checkboxes for various throttle levels, site options, tc elements, etc. Reuse existing Galaxy tools to upload scripts and/or input data. A Special Swift Galaxy Tool: The foreach-tool ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The for-each can enable many workflows with parallel iteration ("foreach") to be composed in Galaxy. Convert Galaxy Workflows to Swift ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A tool that converts existing Galaxy workflow representation to Swift script.