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 [email protected]: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