# -*- coding: utf-8 -*- from SamToBam import SamToBam from StepBase import Configure, Schedule Configure.setRefDir('/home/hca/zhangwei1/hg19_bowtie2') Configure.setGenome('hg19') Configure.setIdentity('ATAC') test = SamToBam(samInput='./minidata/atac/SamForTest', threads=5, bamOutputDir='./bamOutputDir') Schedule.run()
from Bowtie2 import Bowtie2 from AdapterRemoval import AdapterRemoval from StepBase import Configure,Schedule import os Configure.setRefDir('/home/wzhang/genome/hg19_bowtie2/') Configure.setGenome('hg19') #Configure.setIdentity('zwei') Configure.enableDocker(False) rs=Bowtie2(fastqInput1='./minidata/atac/end1', fastqInput2='./minidata/atac/end2') Schedule.run()