Bioinformatic pipelines in Python with Leaf

BMC Bioinformatics

Table 1 Protocol methods summary

Method	Description
clear	Clears a resource from RAM.
clearall	Clears all resources from RAM.
dumpOff	Switches dumping OFF.
dumpOn	Switches dumping ON.
export	Exports the graph to a pdf file, including docstrings.
getinputs	Collects all input resources that are input to the given node and returns a copy of them in a list.
list	Lists the state (unavailable / dumped / to be built) of all resources.
provide	Provides a resource. The resource is returned if available, loaded from disk if dumped, built on the fly otherwise.
publish	Exports the analysis as an HTML bioinformatic protocol.
rebuild	Clears a resource, then provides it.
run	Provides all leaf (final) resources.
trust	Assigns a resource to a node without invalidating dependent resources.
undump	Clears a dumped resource from the disk.
undumpall	Clears all dumped resources from the disk.
untrust	Clears a resource and all its dependent.

This methods are designed to be used through a Python shell to perform pipeline operations. Dumping is the automatic management of produced resources in permanent memory. A resource is said to be available if present in primary memory, dumped if previuosly stored on the disk.

ISSN: 1471-2105