def __init__(self, tree, event, sleepTime, startTime, cpu): Job.__init__(self, cpu=cpu) self.tree = tree self.event = event self.sleepTime = sleepTime self.startTime = startTime self.cpu = cpu
def __init__(self, options, outdir, halfile, genome2seq2len, type): Job.__init__(self) self.options = options self.outdir = outdir self.halfile = halfile self.genome2seq2len = genome2seq2len self.type = type #type has to be bed or wiggle
def __init__(self, halfile, names, outdir, maxOut, minIn): Job.__init__(self) self.halfile = halfile self.names = names self.outdir = outdir self.maxOut = maxOut self.minIn = minIn
def __init__(self, tree, event, sleepTime, startTime, cores): Job.__init__(self, cores=cores) self.tree = tree self.event = event self.sleepTime = sleepTime self.startTime = startTime self.cores = cores
def __init__(self, halfile, tree, bigbeddir, maxOut, minIn): Job.__init__(self) self.halfile = halfile self.tree = tree self.bigbeddir = bigbeddir self.maxOut = maxOut self.minIn = minIn
def __init__(self, genome, seq2len, halfile, outdir, options): Job.__init__(self) self.genome = genome self.seq2len = seq2len self.halfile = halfile self.outdir = outdir self.options = options
def __init__(self, genomes, genome2seq2len, halfile, options, outdir): Job.__init__(self) self.genomes = genomes self.genome2seq2len = genome2seq2len self.halfile = halfile self.options = options self.outdir = outdir
def __init__(self, chromosome, magma_bin, sample_size, annotated_file, daner_file, reference_data): Job.__init__(self, memory="100M", cores=1, disk="100M") self.chromosome = chromosome self.magma_bin = magma_bin self.sample_size = sample_size self.annotated_file = annotated_file self.daner_file = daner_file self.reference_data = reference_data
def __init_(self, cladedir, halfile, query, queryBed, target, chrsizefile): Job.__init__(self) self.cladedir = cladedir self.halfile = halfile self.query = query self.queryBed = queryBed self.target = target self.chrsizefile = chrsizefile
def __init__(self, snp_loc_file): Job.__init__(self, memory="100M", cores=1, disk="100M") self.snp_loc_file = snp_loc_file self.magma_bin = "/Users/vasya/Projects/ripkelab/ricopili/ricopili_bioinfomatics/resources/magma_macOS/magma" self.gene_loc_ref = "/Users/vasya/Projects/ripkelab/ricopili/ricopili_bioinfomatics/resources/magma_macOS/reference_data/NCBI37.3.gene.loc" self.ref_1000g = "/Users/vasya/Projects/ripkelab/ricopili/magma_reference_data/g1000_eur" self.daner_file = "/Users/vasya/Projects/ripkelab/ricopili/ricopili_bioinfomatics/test/resources/pgc_scz_chr22_subset.daner" self.sample_size = "2000"
def __init__(self, genomeoutdir, wig, genome, othergenome, halfile, outdir): Job.__init__(self) self.genomeoutdir = genomeoutdir self.wig = wig self.genome = genome self.othergenome = othergenome self.halfile = halfile self.outdir = outdir
def __init__(self, indir, halfile, genome2seq2len, bigwigdir, noLiftover, outdir): Job.__init__(self) self.indir = indir self.halfile = halfile self.genome2seq2len = genome2seq2len self.bigwigdir = bigwigdir self.noLiftover = noLiftover self.outdir = outdir
def __init__(self, indir, halfile, genome2seq2len, bigbeddir, noLiftover, tab, outdir, options): Job.__init__(self) self.indir = indir self.halfile = halfile self.genome2seq2len = genome2seq2len self.bigbeddir = bigbeddir self.noLiftover = noLiftover self.tab = tab self.outdir = outdir self.options = options
def __init__(self, genomeoutdir, bed, tab, asfile, extrafields, numfield, genome, othergenome, halfile, outdir, options): Job.__init__(self) self.genomeoutdir = genomeoutdir self.bed = bed self.tab = tab self.asfile = asfile self.extrafields = extrafields self.numfield = numfield self.genome = genome self.othergenome = othergenome self.halfile = halfile self.outdir = outdir self.options = options
def __init__(self, dbElem, testFunc, snapshotPath=None, memory="100M", cores=1, disk="100M"): self.dbElem = dbElem self.testFunc = testFunc self.snapshotPath = snapshotPath Job.__init__(self, memory=memory, cores=cores, disk=disk, preemptable=False)
def __init__(self, reads1=None, reads2=None, index=None, indexdir="", quantex="", *args, **kwargs): super(SalmonAlignQuantCls, self).__init__(*args, **kwargs) Job.__init__(self) self.reads1 = reads1 self.reads2 = reads2 self.index = index self.indexdir = indexdir self.quantex = quantex
def __init__(self, step, outputs): Job.__init__(self) self.step = step self.outputs = outputs
def __init__(self): Job.__init__(self, memory=100000, cores=2, disk="3G")
def __init__(self, inputFileID, failFileID): Job.__init__(self, memory=100000, cores=1, disk="1M") self.inputFileID = inputFileID self.failFileID = failFileID
def __init__(self): Job.__init__(self)
def __init__(self, cwlwf, cwljob): Job.__init__(self) self.cwlwf = cwlwf self.cwljob = cwljob
def __init__(self, step, cwljob): Job.__init__(self) self.step = step self.cwljob = cwljob
def __init__(self, cwljob, outdir): Job.__init__(self) self.cwljob = cwljob self.outdir = outdir
def __init__(self, step, cwljob): Job.__init__(self) self.step = step self.cwljob = cwljob self.valueFrom = {shortname(i["id"]): i["valueFrom"] for i in step.tool["inputs"] if "valueFrom" in i}
def __init__(self, cwltool, cwljob): Job.__init__(self) self.cwltool = cwltool self.cwljob = cwljob
def __init__(self, level, foo): Job.__init__(self, memory=100000, cores=2, disk="300M") self.level = level self.foo = foo
def __init__(self, cwlwf, cwljob, basedir): Job.__init__(self) self.cwlwf = cwlwf self.cwljob = cwljob self.basedir = basedir
def __init__(self): Job.__init__(self, memory=1000000, cores=0.01)
def __init__(self, i): Job.__init__(self, memory=200000, cores=0.01) self.i = i
def __init__(self,fileId): Job.__init__(self) self.fileId=fileId
def __init__(self, msg_portion_file_id, trigger_file_id, message_portion_2): Job.__init__(self, memory=100000, cores=1, disk="1M") self.msg_portion_file_id = msg_portion_file_id self.trigger_file_id = trigger_file_id self.message_portion_2 = message_portion_2
def __init__(self, numJobs): Job.__init__(self, memory=100000, cores=0.01) self.numJobs = numJobs
def __init__(self,i): Job.__init__(self, memory=200000, cores=0.01) self.i = i
def __init__(self, fileId): Job.__init__(self) self.fileId = fileId