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
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
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