mkdir -p testing_chia_pipe
cd testing_chia_pipe
git clone https://github.com/TheJacksonLaboratory/ChIA-PIPE.git
wget git@github.com:TheJacksonLaboratory/chia_pipe.zip
cd ChIA-PIPE/
dep_dir="dep_dir"
mkdir $dep_dir
bash local_install_chia_pipe_dependencies.sh -i ${dep_dir}
https://www.dropbox.com/sh/kiunzdfj74dpamh/AAB3u4vVGHIUSZoiPSjEYuYva?dl=0
mkdir -p fastq
cp LDK0004-ds_*.fastq.gz fastq
bash chia_pipe-master/0.chia_pipe_shell.sh -c chia_pipe-master/example_config_file.sh
qsub -F "--conf chia_pipe-master/example_config_file.sh" chia_pipe-master/0.chia_pipe_hpc.pbs