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encodedcc/atac-seq-pipeline:WRN-503_5633333d-7053-4ab9-b02d-146c4cbaf011

Manifest digest

sha256:6323b8bc683d67a9888a857d787588b0eb9b70aa8019a17c4a7b27082d0f5149

OS/ARCH

linux/amd64

Compressed size

937.35 MB

Last pushed

over 2 years by leepc12

Type

Image

Manifest digest

sha256:6323b8bc683d67a9888a857d787588b0eb9b70aa8019a17c4a7b27082d0f5149

Image Layers

Image Layers

1ADD file ... in / 25.45 MB
2/bin/sh -c [ -z "$(apt-get34.54 KB
3/bin/sh -c set -xe &&848 B
4/bin/sh -c mkdir -p /run/systemd162 B
5CMD ["/bin/bash"]0 B
6MAINTAINER Jin Lee0 B
7ENV DEBIAN_FRONTEND=noninteractive0 B
8RUN /bin/sh -c apt-get update443.14 MB
9RUN /bin/sh -c mkdir /software98 B
10WORKDIR /software32 B
11ENV PATH=/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
12RUN /bin/sh -c wget https://github.com/openssl/openssl/archive/OpenSSL_1_0_2t.tar.gz9.29 MB
13RUN /bin/sh -c pip3 install45.1 MB
14RUN /bin/sh -c pip3 install82.28 MB
15RUN /bin/sh -c echo "r3.35 MB
16RUN /bin/sh -c wget "https://cran.r-project.org/src/contrib/Archive/caTools/caTools_1.17.1.4.tar.gz"191.85 KB
17RUN /bin/sh -c Rscript -e59.07 MB
18RUN /bin/sh -c wget https://github.com/hms-dbmi/spp/archive/1.15.tar.gz710.65 KB
19RUN /bin/sh -c git clone1.9 MB
20RUN /bin/sh -c git clone12.15 MB
21RUN /bin/sh -c wget https://github.com/broadinstitute/picard/releases/download/2.20.7/picard.jar14.61 MB
22RUN /bin/sh -c wget https://github.com/lomereiter/sambamba/releases/download/v0.6.6/sambamba_v0.6.6_linux.tar.bz21.23 MB
23RUN /bin/sh -c wget http://gnu.mirror.vexxhost.com/gsl/gsl-1.16.tar.gz8.2 MB
24ENV LD_LIBRARY_PATH=:/usr/local/lib0 B
25RUN /bin/sh -c git clone243.24 KB
26RUN /bin/sh -c wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip48.31 MB
27RUN /bin/sh -c git clone528.59 KB
28RUN /bin/sh -c wget https://github.com/kundajelab/phantompeakqualtools/archive/1.2.1.tar.gz121.41 KB
29ENV PATH=/software/phantompeakqualtools-1.2.1:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
30RUN /bin/sh -c pip3 install369.27 KB
31RUN /bin/sh -c git clone109.31 KB
32RUN /bin/sh -c pip2 install65.86 MB
33RUN /bin/sh -c pip3 install3.18 MB
34RUN /bin/sh -c pip3 install2.73 MB
35RUN /bin/sh -c pip3 install1.76 MB
36RUN /bin/sh -c pip2 install3.66 MB
37RUN /bin/sh -c pip2 install18.62 MB
38RUN /bin/sh -c pip2 install30.04 MB
39RUN /bin/sh -c git clone11.53 MB
40ENV PATH=/software/phantompeakqualtools-1.2.1:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/software/kentUtils_bin_v377/bin0 B
41ENV LD_LIBRARY_PATH=:/usr/local/lib:/software/kentUtils_bin_v377/lib0 B
42RUN /bin/sh -c wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip116.64 KB
43RUN /bin/sh -c pip3 install944.25 KB
44RUN /bin/sh -c mkdir bedops_2.4.3926.36 MB
45ENV PATH=/software/bedops_2.4.39/bin:/software/phantompeakqualtools-1.2.1:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/software/kentUtils_bin_v377/bin0 B
46RUN /bin/sh -c pip3 install16.15 MB
47ENV PYTHONNOUSERSITE=True0 B
48ENV OPENBLAS_NUM_THREADS=10 B
49ENV MKL_NUM_THREADS=10 B
50RUN /bin/sh -c mkdir -p120 B
51RUN /bin/sh -c mkdir -p148 B
52ENV PATH=/software/atac-seq-pipeline:/software/atac-seq-pipeline/src:/software/bedops_2.4.39/bin:/software/phantompeakqualtools-1.2.1:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/software/kentUtils_bin_v377/bin0 B
53RUN /bin/sh -c mkdir -p184 B
54ENV PYTHONPATH=/software/atac-seq-pipeline/src0 B
55COPY src atac-seq-pipeline/src/ # buildkit60.96 KB
56COPY atac.wdl atac-seq-pipeline/ # buildkit18.52 KB
57COPY dev/test/test_py atac-seq-pipeline/dev/test/test_py/ # buildkit220 B

Command

ADD file:c477cb0e95c56b51e0b7353f3805165393689902b82a41bbe77dbef4b31667e1 in /