ChIA-PIPE README The Jackson Laboratory for Genomic Medicine Version 1.0, (November 26, 2018) (a) Initialize outer working directory mkdir -p testing_chia_pipe cd testing_chia_pipe (b) Clone ChIA-PIPE git clone https://github.com/TheJacksonLaboratory/ChIA-PIPE.git or (b.ii) Download ChIA-PIPE wget git@github.com:TheJacksonLaboratory/chia_pipe.zip (c) Install ChIA-PIPE dependencies cd ChIA-PIPE/ dep_dir="dep_dir" mkdir $dep_dir bash local_install_chia_pipe_dependencies.sh -i ${dep_dir} (d) Download test data from Dropbox https://www.dropbox.com/sh/kiunzdfj74dpamh/AAB3u4vVGHIUSZoiPSjEYuYva?dl=0 mkdir -p fastq cp LDK0004-ds_*.fastq.gz fastq (e) Launch ChIA-PIPE bash chia_pipe-master/0.chia_pipe_shell.sh -c chia_pipe-master/example_config_file.sh or (e.ii) Launch ChIA-PIPE on HPC qsub -F "--conf chia_pipe-master/example_config_file.sh" chia_pipe-master/0.chia_pipe_hpc.pbs