.config.yaml

general:
  custom_tmp_dir: /tmp/

# Good source for standard builds & paths is the Illumina iGenomes collection:
#   http://support.illumina.com/sequencing/sequencing_software/igenome.html
bowtie2_genomes:
  mm9: Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome
  mm10: Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
  hg18: Mus_musculus/UCSC/hg18/Sequence/Bowtie2Index/genome
  hg19: Mus_musculus/UCSC/hg19/Sequence/Bowtie2Index/genome

# Binaries -- some distributed with this package
# We include these to try to standardize on sane versions of software.
binaries:
  samtools: dist/samtools-1.2
  samtools_legacy: dist/samtools-0.1.19
  bedtools: dist/bedtools-2.23.0
  findPeaks: dist/findPeaks-4.7  # via http://homer.salk.edu/homer/

# Blacklisting paths
# From the ENCODE blacklist of known overcalled/false-positive regions.
blacklists:
  mm9: blacklists/mm9-blacklist.bed
  mm10: blacklists/mm10-blacklist-via-mm9.bed
  hg19: blacklists/wgEncodeDacMapabilityConsensusExcludable.bed
  ce10: blacklists/ce10-blacklist.bed
  dm3: blacklists/dm3-blacklist.bed

# RefSeq maps, for the RIESLING code, via UCSC
refseq:
  mm9: refseq/mm9.ucsc.RefSeq.refGene.tsv.gz
  mm10: refseq/mm10.ucsc.RefSeq.refGene.tsv.gz
  hg18: refseq/hg18.ucsc.RefSeq.refGene.tsv.gz
  hg19: refseq/hg19.ucsc.RefSeq.refGene.tsv.gz
  hg38: refseq/hg38.ucsc.RefSeq.refGene.tsv.gz

# Gene info, for final annotation steps of RIESLING
gffs:
  mm9: /dev/null
  mm10: genomes/mm10genes.transcript.gtf
  hg18: /dev/null
  hg19: /dev/null