text: RAWDATA_DIR = '/staging/as/skchoudh/re-ribo-datasets/mm10/SRP076538'
  OUT_DIR = '/staging/as/skchoudh/re-ribo-analysis/mm10/SRP076538'
  GENOME_FASTA = '/home/cmb-06/as/skchoudh/genomes/mm10/fasta/Mus_musculus.GRCm38.dna.primary_assembly.fa'
  CHROM_SIZES = '/home/cmb-06/as/skchoudh/genomes/mm10/fasta/Mus_musculus.GRCm38.dna.primary_assembly.sizes'
  STAR_INDEX = '/home/cmb-06/as/skchoudh/genomes/mm10/star_annotated_ribopod'
  GTF_VERSION = 'v96'
  GTF = '/home/cmb-06/as/skchoudh/genomes/mm10/annotation/Mus_musculus.GRCm38.96.chr_patch_hapl_scaff.gtf'
  GENE_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/v96/gene.bed.gz'
  STAR_CODON_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/v96/start_codon.bed.gz'
  STOP_CODON_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/v96/stop_codon.bed.gz'
  CDS_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/v96/cds.bed.gz'
  UTR5_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/v96/utr5.bed.gz'
  UTR3_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/v96/utr3.bed.gz'
  INTRON_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/v96/intron.bed.gz'
  ORIENTATIONS = ['5prime', '3prime']
  STRANDS = ['pos', 'neg', 'combined']
  FRAGMENT_LENGTHS =  range(18, 39)
  RIBOTRICER_ANNOTATION_PREFIX = '/home/cmb-06/as/skchoudh/genomes/mm10/ribotricer_v96_annotation_longest'
  