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encodedcc/atac-seq-pipeline:PIPE-83_fix-zero-length-read_77b463cf-fc6e-4238-8b39-e55f595742c1

Manifest digest

sha256:9bb1a01519f19f87921925b99a5db2e429717e9195adf627057582fe5cc812e9

OS/ARCH

linux/amd64

Compressed size

919.34 MB

Last pushed

over 3 years by leepc12

Type

Image

Manifest digest

sha256:9bb1a01519f19f87921925b99a5db2e429717e9195adf627057582fe5cc812e9

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
8/bin/sh -c apt-get update &&418.2 MB
9/bin/sh -c mkdir /software97 B
10WORKDIR /software0 B
11ENV PATH=/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
12/bin/sh -c wget https://github.com/openssl/openssl/archive/OpenSSL_1_0_2t.tar.gz &&9.29 MB
13/bin/sh -c pip3 install --no-cache-dir53.22 MB
14/bin/sh -c pip3 install --no-cache-dir74.81 MB
15/bin/sh -c echo "r <-3.51 MB
16/bin/sh -c Rscript -e "source('http://bioconductor.org/biocLite.R');57.05 MB
17/bin/sh -c wget https://github.com/hms-dbmi/spp/archive/1.15.tar.gz &&710.28 KB
18/bin/sh -c git clone --branch1.9 MB
19/bin/sh -c git clone --branch12.15 MB
20/bin/sh -c wget https://github.com/broadinstitute/picard/releases/download/2.20.7/picard.jar &&14.61 MB
21/bin/sh -c wget https://github.com/lomereiter/sambamba/releases/download/v0.6.6/sambamba_v0.6.6_linux.tar.bz2 &&1.23 MB
22/bin/sh -c wget http://gnu.mirror.vexxhost.com/gsl/gsl-1.16.tar.gz &&8.2 MB
23ENV LD_LIBRARY_PATH=:/usr/local/lib0 B
24/bin/sh -c git clone --branch243.25 KB
25/bin/sh -c wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip &&48.31 MB
26/bin/sh -c git clone --branch528.71 KB
27/bin/sh -c wget https://github.com/kundajelab/phantompeakqualtools/archive/1.2.1.tar.gz &&121.41 KB
28ENV PATH=/software/phantompeakqualtools-1.2.1:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
29/bin/sh -c pip3 install --no-cache-dir350.77 KB
30/bin/sh -c git clone --branch109.3 KB
31/bin/sh -c pip2 install --no-cache-dir65.85 MB
32/bin/sh -c pip3 install --no-cache-dir3.18 MB
33/bin/sh -c pip2 install --no-cache-dir48.44 MB
34/bin/sh -c pip3 install --no-cache-dir92 B
35/bin/sh -c pip3 install --no-cache-dir1.76 MB
36/bin/sh -c git clone https://github.com/ENCODE-DCC/kentUtils_bin_v37711.53 MB
37ENV 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
38ENV LD_LIBRARY_PATH=:/usr/local/lib:/software/kentUtils_bin_v377/lib0 B
39/bin/sh -c wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip &&116.64 KB
40/bin/sh -c pip3 install --no-cache-dir979.07 KB
41/bin/sh -c mkdir bedops_2.4.39 &&26.36 MB
42ENV 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
43/bin/sh -c pip3 install --no-cache-dir31.07 MB
44ENV PYTHONNOUSERSITE=True0 B
45ENV OPENBLAS_NUM_THREADS=10 B
46ENV MKL_NUM_THREADS=10 B
47/bin/sh -c mkdir -p /mnt/ext_{0..9}153 B
48/bin/sh -c mkdir -p atac-seq-pipeline/src177 B
49ENV 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
50/bin/sh -c mkdir -p atac-seq-pipeline/dev/test/test_py215 B
51ENV PYTHONPATH=/software/atac-seq-pipeline/src0 B
52COPY dir:940827286d626d6a2028da00f6c83ada061c6c7874052db354a7f60fa61c258f in atac-seq-pipeline/src/ 60.97 KB
53COPY file:f9d08b1221277d3415250746b3bbd84d65eba6d87f4f8a1e91d39fb0b93f2dd2 in atac-seq-pipeline/ 18.52 KB
54COPY dir:c34242295790de6a582d5d275e50da3bd308ddaddad38428541f5b266d1f4061 in atac-seq-pipeline/dev/test/test_py/ 225 B

Command

ADD file:c477cb0e95c56b51e0b7353f3805165393689902b82a41bbe77dbef4b31667e1 in /