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.

Napolitano et al.

Napolitano et al. BMC Bioinformatics 2013 14:201   doi:10.1186/1471-2105-14-201

Open Data