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johnegarza/immuno-testing:latest

Manifest digest

sha256:83f5b6eda948f53d9a725b0e66af0ed91d101dab63463464ea92d5c48673215d

OS/ARCH

linux/amd64

Compressed size

704.63 MB

Last pushed

over 7 years by johnegarza

Type

Image

Manifest digest

sha256:83f5b6eda948f53d9a725b0e66af0ed91d101dab63463464ea92d5c48673215d

Image Layers

Image Layers

1ADD file ... in / 40.97 MB
2/bin/sh -c set -xe &&847 B
3/bin/sh -c rm -rf /var/lib/apt/lists/*620 B
4/bin/sh -c sed -i 's/^#\s*\(deb.*universe\)$/\1/g'854 B
5/bin/sh -c mkdir -p /run/systemd169 B
6CMD ["/bin/bash"]0 B
7LABEL base.image=ubuntu:16.040 B
8LABEL version=40 B
9LABEL software=Biocontainers base Image0 B
10LABEL software.version=082520160 B
11LABEL description=Base image for0 B
12LABEL website=http://biocontainers.pro0 B
13LABEL documentation=https://github.com/BioContainers/specs/wiki0 B
14LABEL license=https://github.com/BioContainers/containers/blob/master/LICENSE0 B
15LABEL tags=Genomics,Proteomics,Transcriptomics,General,Metabolomics0 B
16MAINTAINER Felipe da Veiga0 B
17ENV DEBIAN_FRONTEND=noninteractive0 B
18/bin/sh -c mv /etc/apt/sources.list /etc/apt/sources.list.bkp956 B
19/bin/sh -c apt-get clean all243.82 MB
20/bin/sh -c echo 'export PATH=/opt/conda/bin:$PATH'31.14 MB
21/bin/sh -c TINI_VERSION=`curl https://github.com/krallin/tini/releases/latest |579.54 KB
22/bin/sh -c mkdir /data /config112 B
23/bin/sh -c groupadd fuse &&4.64 KB
24/bin/sh -c chmod 777 -R31.14 MB
25USER [biodocker]0 B
26ENV PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/conda/bin0 B
27ENV PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/conda/bin:/home/biodocker/bin0 B
28ENV HOME=/home/biodocker0 B
29/bin/sh -c mkdir /home/biodocker/bin142 B
30/bin/sh -c conda config --add7.3 KB
31/bin/sh -c conda config --add229 B
32/bin/sh -c conda upgrade conda41.97 MB
33VOLUME [/data /config]0 B
34CMD ["/bin/bash"]0 B
35WORKDIR /data0 B
36USER [root]0 B
37/bin/sh -c apt-get update &&64.2 MB
38/bin/sh -c curl -O https://support.hdfgroup.org/ftp/HDF5/current18/bin/hdf5-1.8.20-linux-centos7-x86_64-gcc485-shared.tar.gz28.86 MB
39ENV LD_LIBRARY_PATH=/usr/local/lib:0 B
40ENV HDF5_DIR=/usr/local/0 B
41/bin/sh -c pip install --upgrade75.47 MB
42/bin/sh -c git clone https://github.com/FRED-2/OptiType.git24.85 MB
43/bin/sh -c git clone https://github.com/seqan/seqan.git2.09 MB
44ENV PATH=/usr/local/bin/OptiType:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/conda/bin:/home/biodocker/bin0 B
45USER [biodocker]0 B
46WORKDIR /data/0 B
47ENTRYPOINT ["OptiTypePipeline.py"]0 B
48CMD ["-h"]0 B
49MAINTAINER Benjamin Schubert <[email protected]>0 B
50MAINTAINER John Garza <[email protected]>0 B
51LABEL description=Image containing optitype0 B
52USER root0 B
53/bin/sh -c apt-get update -y47.57 MB
54ENV HTSLIB_INSTALL_DIR=/opt/htslib0 B
55WORKDIR /tmp0 B
56/bin/sh -c wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2 &&1.98 MB
57WORKDIR /tmp/htslib-1.3.20 B
58/bin/sh -c ./configure --enable-plugins18.87 MB
59ENV SAMTOOLS_INSTALL_DIR=/opt/samtools0 B
60WORKDIR /tmp0 B
61/bin/sh -c wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 &&8.45 MB
62WORKDIR /tmp/samtools-1.3.10 B
63/bin/sh -c ./configure --with-htslib=$HTSLIB_INSTALL_DIR --prefix=$SAMTOOLS_INSTALL_DIR3.5 MB
64WORKDIR /0 B
65/bin/sh -c rm -rf /tmp/samtools-1.3.1135 B
66/bin/sh -c mkdir /opt/sambamba/ 2.83 MB
67ENV BWA_VERSION=0.7.150 B
68/bin/sh -c cd /tmp/ 717.75 KB
69WORKDIR /usr/bin/0 B
70/bin/sh -c wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools12.09 MB
71/bin/sh -c chmod +x bedtools12.09 MB
72COPY file:0765b131b37f6bc17232c4f48711fd68a5c2735094cb2cd477de1ffafa8e1f20 in /usr/bin/optitype_script.sh 1.08 KB
73/bin/sh -c mkdir -p /ref_data/optitype_ref126 B
74/bin/sh -c mkdir -p /ref_data/ebi_ref121 B
75COPY file:aa7f717d1d14a2ba1f3a091b6fde4c7c51e8c780e227463bb625073dba6ebae2 in /ref_data/optitype_ref/hla_reference_dna.fasta 423.38 KB
76COPY file:27cef4e9a5104e6e388eb7ba3dd69b2c5efddf6607a41065fd3ae75f79f0cd53 in /ref_data/optitype_ref/hla_reference_dna.fasta.amb 200 B
77COPY file:e77f37d6aef7711108771369b58c967fa509fab70e6873eeb500f236491519cb in /ref_data/optitype_ref/hla_reference_dna.fasta.ann 140.29 KB
78COPY file:b9d5f6aa8cb5a52259fd286ef22981ae40b2cea02730430a701e13fcac2f0112 in /ref_data/optitype_ref/hla_reference_dna.fasta.bwt 1.03 MB
79COPY file:54c5ae406f301e2aeab58ba52770366962d7f74f474ca57bed3e764fe3e1239e in /ref_data/optitype_ref/hla_reference_dna.fasta.pac 205.27 KB
80COPY file:be0645ce8a873a57a1e5d88b9ef12702640876a669bd9df9ddf37a16eb853f4d in /ref_data/optitype_ref/hla_reference_dna.fasta.sa 4.01 MB
81COPY file:3dd0a281e188bd971adaa4d649273bdc3fb483878ab635a364c5fb1c059530ae in /ref_data/ebi_ref/hla_nuc.fasta 414.19 KB
82COPY file:bf5f08da97407e70fe442204589de30ef0bcc359c10117a1dd3a757e1c42d4d0 in /ref_data/ebi_ref/hla_nuc.fasta.amb 189 B
83COPY file:8d54540606f8f902f3d4dee05011acb32dbec3f60761fac3f266922e5b121407 in /ref_data/ebi_ref/hla_nuc.fasta.ann 224.14 KB
84COPY file:e3107fef8925285259849f77a532a8fdc0a10c62d90f041a0373d0116a8d61f7 in /ref_data/ebi_ref/hla_nuc.fasta.bwt 1.39 MB
85COPY file:af14c93f9bed6522c248378afedc0047e95d8de54153691c6bfc73a5535b4c70 in /ref_data/ebi_ref/hla_nuc.fasta.pac 185.95 KB
86COPY file:25dd82fc57256999a32fc93920384a6493be383f6bff81bcb1405466500e5691 in /ref_data/ebi_ref/hla_nuc.fasta.sa 3.48 MB
87ENTRYPOINT []0 B
88CMD []0 B

Command

ADD file:c753df38640ab6e246d9e66f0cef7156b7003976080b1e0b83e5717cd6ef1725 in /