rnakato/juicer

docker_juicer

Juicer分析的Docker镜像仓库。GitHub地址：https://github.com/rnakato/docker_juicer

运行

Docker

bash
# 拉取镜像
docker pull docker.xuanyuan.run/rnakato/juicer

# 容器登录
docker run [--gpus all] --rm -it rnakato/juicer /bin/bash
# 执行命令
docker run [--gpus all] --rm -v (你的目录):/opt/work rnakato/juicer <命令>

Singularity

bash
# 构建镜像
singularity build -F rnakato_juicer.sif docker://rnakato/juicer 
# 执行命令
singularity exec [--nv] rnakato_juicer.sif <命令>

使用方法

脚本假设fastq文件存储在fastq/$cell（例如fastq/Control_1）。输出结果存储在JuicerResults/$cell。

BWA索引文件应位于/work/Database/bwa-indexes/UCSC-$build。

使用Singularity镜像（rnakato_juicer.sif）的完整命令如下：

bash
build=hg38
fastq_post="_R"  # .fastq.gz前的"_"或"_R"
enzyme=MboI      # 酶类型

gt=genome_table.$build.txt  # genome_table文件
gene=refFlat.$build.txt # 基因注释（refFlat格式）
sing="singularity exec rnakato_juicer.sif"  # singularity命令

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

    # 通过Juicer生成.hic文件
    $sing juicer_map.sh $odir $build $enzyme $fastq_post

    # 绘制接触频率
    if test ! -e $odir/distance; then $sing plot_distance_count.sh $cell $odir; fi

    # 选择归一化类型
    norm=VC_SQRT

    # 为染色体构建接触矩阵
    hic=$odir/aligned/inter_30.hic
    if test ! -e $odir/Matrix; then
        $sing juicer_makematrix.sh $norm $hic $odir $gt
    fi

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

    # 计算Pearson系数和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

    # 计算绝缘分数
    if test ! -e $odir/InsulationScore; then $sing juicer_insulationscore.sh $norm $odir $gt; fi

    # 调用环（HICCUPS，添加'--nv'选项以使用GPU）
    singularity exec --nv rnakato_juicer.sif call_HiCCUPS.sh $norm $odir $hic $build
    # 基序分析
    $sing juicertools.sh motifs $build $motifdir $odir/loops/$norm/merged_loops.bedpe hg38.motifs.txt
done

从Dockerfile构建镜像

首先克隆仓库并进入目录

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

然后执行：

bash
docker build -t <账户名>/juicer .

联系方式

Ryuichiro Nakato: rnakato AT iqb.u-tokyo.ac.jp