new_contents: GENOMES_DIR='/media/data1/genomes'
  OUT_DIR = '/media/data2/HuR_human_mouse/mouse/ribo-seq'
  SRC_DIR = '/home/saket/github_projects/clip_seq_pipeline/scripts'
  RAWDATA_DIR ='/media/data1/HuR_human_mouse/mouse/ribo/Penalva_L_03222017'
  GENOME_BUILD = 'mm10'
  GENOME_FASTA = GENOMES_DIR + '/' + GENOME_BUILD + '/fasta/'+ GENOME_BUILD+ '.fa'
  STAR_INDEX = GENOMES_DIR + '/' + GENOME_BUILD + '/star_annotated'
  GTF = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.vM11.annotation.without_rRNA_tRNA.gtf'
  GENE_NAMES = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + GENOME_BUILD+'_gene_names_stripped.tsv'
  GENE_LENGTHS = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.vM11.coding_lengths.tsv'  #+ GENOME_BUILD+'_gene_lengths.tsv'
  DESIGN_FILE = RAWDATA_DIR + '/' + 'design.txt'
  HTSEQ_STRANDED = 'yes'
  FEATURECOUNTS_S = '-s 1'
  GENE_BED = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.vM11.genes.fromucsc.bed'  #+ GENOME_BUILD+'_gene_lengths.tsv'
  FEATURECOUNTS_T='cds'
  HTSEQ_MODE='union'
  
subject: add mouse config