Packaged WorkflowsΒΆ

When SyQADA tries to resolve the path to a taskfile or template file that it finds in a protocol file or a task file, it looks for the file first in the local directory. If it does not find it there, SyQADA appends the path to each element of the environment variable, SYQADAPATH, so that workflow files can located elsewhere in the file system than the current directory. By default, SYQADAPATH is set to $SYQADA. This allows the protocol file and the task files to specify task and template files directly from the installed workflows directory, which will usually work fine for well-established workflows.

A repository of workflows is to be found in the $SYQADA/resources/workflows directory, subdivided into general topic. At lower levels of the tree, there are tasks and templates directories holding the task files and the templates they invoke. Each general topic branch directory usually contains a protocols directory, which contains protocols employing those task files and sometimes their config files.