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How to setup the TOuCAN configuration file

Environment variables

• path_bowtie2

  • Path to directory where bowtie2 is installed. For example: "/mnt/software/x86_64/packages/bowtie2/2.3.3.1/".
    Do not add the executable to the path.

• path_python

  • Path to directory where python is installed. For example: "/mnt/software/x86_64/packages/python/2.7.8/bin".
    Do not add the executable to the path.

• path_bwa

  • Path to directory where bwa is installed. For example: "/mnt/software/x86_64/packages/bwa/0.7.12/bin".
    Do not add the executable to the path.

• path_bwa

  • Path to directory where bwa is installed. For example: "/mnt/software/x86_64/packages/bwa/0.7.12/bin".
    Do not add the executable to the path.

• path_samtools

  • Path to directory where SAMtools is installed. For example: "/mnt/software/x86_64/packages/samtools/1.3.1/bin".
    Do not add the executable to the path.

• path_bedtools

  • Path to directory where BEDtools is installed. For example: "/mnt/software/x86_64/packages/bedtools/2.27.1/bin".
    Do not add the executable to the path.

• path_bin

  • Path to bin directory of TOuCAN . For example: "./TOuCAN/bin". *path_genome
  • Path to full genome in fasta format + bwa index. The name of the fasta file has to be the basename of the bwa index. For example:
    ./index_bwa/ ./GRCm38.p5.genome_whitelist.fa ./GRCm38.p5.genome_whitelist.fa ./GRCm38.p5.genome_whitelist.fa ./GRCm38.p5.genome_whitelist.fa ./GRCm38.p5.genome_whitelist.fa ./GRCm38.p5.genome_whitelist.fa ./GRCm38.p5.genome_whitelist.fa ./GRCm38.p5.genome_whitelist.fa ./GRCm38.p5.genome_whitelist.fa amb .ann .bwt .pac .rbwt .rpac .rsa .sa