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, 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, 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):
Job.__init__(self, memory=100000, cores=2, disk="3G")
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, inputFileID, failFileID):
Job.__init__(self, memory=100000, cores=1, disk="1M")
self.inputFileID = inputFileID
self.failFileID = failFileID
def __init__(self, cwlwf, cwljob, basedir):
Job.__init__(self)
self.cwlwf = cwlwf
self.cwljob = cwljob
self.basedir = basedir
def __init__(self, cwlwf, cwljob):
Job.__init__(self)
self.cwlwf = cwlwf
self.cwljob = cwljob
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, cwltool, cwljob):
Job.__init__(self)
self.cwltool = cwltool
self.cwljob = cwljob
def __init__(self, cwljob, outdir):
Job.__init__(self)
self.cwljob = cwljob
self.outdir = outdir
def __init__(self, step, outputs):
Job.__init__(self)
self.step = step
self.outputs = outputs
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, cwlwf, cwljob, basedir):
Job.__init__(self)
self.cwlwf = cwlwf
self.cwljob = cwljob
self.basedir = basedir
def __init__(self, numJobs):
Job.__init__(self, memory=100000, cores=0.01)
self.numJobs = numJobs
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):
Job.__init__(self)
def __init__(self, numJobs):
Job.__init__(self, memory=100000, cores=0.01)
self.numJobs = numJobs
def __init__(self, fileId):
Job.__init__(self)
self.fileId = fileId
def __init__(self, step, cwljob):
Job.__init__(self)
self.step = step
self.cwljob = cwljob
