def __init__(self, primer3_dir="", trf_dir="", primer3_bin="primer3_core", trf_bin="trf", glistmaker_dir="", glistmaker_bin="glistmaker", primer3_thermo_config_dir=None): Pipeline.__init__(self) self.primer3_dir = primer3_dir self.trf_dir = trf_dir self.primer3_bin = primer3_bin self.trf_bin = trf_bin self.glistmaker_dir = glistmaker_dir self.glistmaker_bin = glistmaker_bin self.primer3_thermo_config_dir = primer3_thermo_config_dir
def __init__(self, max_threads=1, max_memory=10, GATK_dir="", GATK_jar="GenomeAnalysisTK.jar", Picard_dir=""): Pipeline.__init__(self, max_threads=max_threads, max_memory=max_memory) self.GATK_dir = GATK_dir self.GATK_jar = GATK_jar self.Picard_dir = Picard_dir
def __init__(self, max_threads=1, max_memory=10, BWA_dir="", BWA_binary=None, bowtie2_dir="", bowtie2_binary=None, Picard_dir=""): Pipeline.__init__(self, max_threads=max_threads, max_memory=max_memory) self.BWA_dir = BWA_dir self.bowtie2_dir = bowtie2_dir self.Picard_dir = Picard_dir self.BWA_binary = BWA_binary self.bowtie2_binary = bowtie2_binary
def __init__(self, workdir="./", max_threads=1): Pipeline.__init__(self, workdir=workdir, max_threads=max_threads) self.dirs = { "fastq": { "raw": [], "trimmed": [], }, "fasta": { "raw": [], "trimmed": [], }, "qual_plot": { "raw": [], "trimmed": [], }, } self.sanger_extention_list = [".ab1"]
from Pipelines.Abstract import Pipeline from Pipelines.Filtering import FilteringPipeline from Pipelines.DiffExpression import DiffExpressionPipeline Pipeline = Pipeline() FilteringPipeline = FilteringPipeline() DiffExpressionPipeline = DiffExpressionPipeline()
def __init__(self): Pipeline.__init__(self)