Python Configure.setRefDir Examples

Example #1

# -*- 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()

Example #2

File: test_Bowtie2_1.py Project: chansigit/zuoye

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()