rnakato/juicer repository overview

# pull docker image
docker pull rnakato/juicer

# container login
docker run [--gpus all] --rm -it rnakato/juicer /bin/bash
# execute a command
docker run [--gpus all] --rm -v (your directory):/opt/work rnakato/juicer <command>

# build image
singularity build -F rnakato_juicer.sif docker://rnakato/juicer 
# execute a command
singularity exec [--nv] rnakato_juicer.sif <command>

build=hg38
fastq_post="_R"  # "_" or "_R"  before .fastq.gz
enzyme=MboI      # enzyme type

gt=genome_table.$build.txt  # genome_table file
gene=refFlat.$build.txt # gene annotation (refFlat format)
sing="singularity exec rnakato_juicer.sif"  # singularity command

for cell in `ls fastq/* -d | grep -v .sh`
do
    cell=$(basename $cell)
    odir=$(pwd)/JuicerResults/$cell
    echo $cell

    rm -rf $odir
    mkdir -p $odir
    if test ! -e $odir/fastq; then ln -s $(pwd)/fastq/$cell/ $odir/fastq; fi

    # generate .hic file by Juicer
    $sing juicer_map.sh $odir $build $enzyme $fastq_post

    # plot contact frequency
    if test ! -e $odir/distance; then $sing plot_distance_count.sh $cell $odir; fi

    # select normalization type
    norm=VC_SQRT
    
    # make contact matrix for chromosomes
    hic=$odir/aligned/inter_30.hic
    if test ! -e $odir/Matrix; then
        $sing juicer_makematrix.sh $norm $hic $odir $gt
    fi

    # call TADs (arrowHead)
    if test ! -e $odir/TAD; then
        $sing juicer_callTAD.sh $norm $hic $odir $gt
    fi

    # calculate Pearson coefficient and Eigenvector
    for resolution in 25000
    do
            $sing makeEigen.sh Pearson $norm $odir $hic $resolution $gt $gene
            $sing makeEigen.sh Eigen $norm $odir $hic $resolution $gt $gene
    done
    
    # calculate insulation score
    if test ! -e $odir/InsulationScore; then $sing juicer_insulationscore.sh $norm $odir $gt; fi
    
    # call loops (HICCUPS, add '--nv' option to use GPU)
    singularity exec --nv rnakato_juicer.sif call_HiCCUPS.sh $norm $odir $hic $build
    # motif analysis
    $sing juicertools.sh motifs $build $motifdir $odir/loops/$norm/merged_loops.bedpe hg38.motifs.txt
done

git clone https://github.com/rnakato/docker_juicer.git
cd docker_juicer

docker build -t <account>/juicer .