Lathe

Dynamic build system.

Lathe allows a user to programatically define a workflow of tasks.

The lathe build files are written in JavaScript.

Example:

prep = lathe.Workflow("prep")

projects = [
    {name: "BeatAML_2018"},
    {name: "FIMM_2016"},
    {name: "NCI60_2021"},
    {name: "Tavor_2020"},
    {name: "CCLE_2015"},
    {name: "GBM_scr2"},
    {name: "PDTX_2019"},
    {name: "UHNBreast_2019"},
    {name: "CTRPv2_2015"},
    {name: "GBM_scr3"},
    {name: "GRAY_2017"},
    {name: "PRISM_2020"},
    {name: "gCSI_2019"}
]

downloadOutputs = {}

projects.forEach( (element, index) => {
    downloadOutputs[`file_${index}`] = `../../source/pharmacodb/rdata/${element.name}.rdata`
})

p = lathe.Process({
    name: "download",
    commandLine: `cwltool --outdir ../../source/pharmacodb/rdata ./download_pharmaco.cwl`,
    outputs: downloadOutputs
})
prep.Add(p)

Lathe Object

	Params: map[string]string{}
	Workflow:    function(name)
	LoadPlan:    function(path)
	Process:     function(Process)
	File:        function(path)
	Plugin:      function(commandLine)
	DockerImage: function(path)

Process Object

	BasePath    string
	Name        string
	Desc        map[string]any
	CommandLine string
	Inputs      map[string]string
	Outputs     map[string]string
	MemMB       uint
	NCpus       uint

Running lathe

lathe run <lathe_file> <workflow_name>