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chrisamiller/docker-genomic-analysis:0.2

Manifest digest

sha256:95232e34b833bb55cecde0135eaf4b89d456e7a11aecf9e234857468bf74deed

OS/ARCH

linux/amd64

Compressed size

2.93 GB

Last pushed

almost 5 years by chrisamiller

Type

Image

Manifest digest

sha256:95232e34b833bb55cecde0135eaf4b89d456e7a11aecf9e234857468bf74deed

Image Layers

Image Layers

1ADD file ... in / 27.24 MB
2CMD ["bash"]0 B
3LABEL org.opencontainers.image.licenses=GPL-2.0-or-later org.opencontainers.image.source=https://github.com/rocker-org/rocker-versioned2 org.opencontainers.image.vendor=Rocker Project0 B
4ENV R_VERSION=4.1.20 B
5ENV TERM=xterm0 B
6ENV LC_ALL=en_US.UTF-80 B
7ENV LANG=en_US.UTF-80 B
8ENV R_HOME=/usr/local/lib/R0 B
9ENV CRAN=https://packagemanager.rstudio.com/all/__linux__/focal/latest0 B
10ENV TZ=Etc/UTC0 B
11COPY scripts/install_R.sh /rocker_scripts/install_R.sh # buildkit1.86 KB
12RUN /bin/sh -c /rocker_scripts/install_R.sh #282.35 MB
13COPY scripts /rocker_scripts # buildkit22.46 KB
14RUN /bin/sh -c /rocker_scripts/patch_install_command.sh #187 B
15CMD ["R"]0 B
16LABEL org.opencontainers.image.licenses=GPL-2.0-or-later org.opencontainers.image.source=https://github.com/rocker-org/rocker-versioned2 org.opencontainers.image.vendor=Rocker Project0 B
17ENV S6_VERSION=v2.1.0.20 B
18ENV RSTUDIO_VERSION=2021.09.0+3510 B
19ENV DEFAULT_USER=rstudio0 B
20ENV PATH=/usr/lib/rstudio-server/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
21RUN /bin/sh -c /rocker_scripts/install_rstudio.sh #201.76 MB
22RUN /bin/sh -c /rocker_scripts/install_pandoc.sh #25.94 KB
23EXPOSE map[8787/tcp:{}]0 B
24CMD ["/init"]0 B
25ARG BIOCONDUCTOR_VERSION=3.140 B
26ARG BIOCONDUCTOR_PATCH=300 B
27ARG BIOCONDUCTOR_DOCKER_VERSION=3.14.300 B
28LABEL name=bioconductor/bioconductor_docker version=3.14.30 url=https://github.com/Bioconductor/bioconductor_docker vendor=Bioconductor0 B
29RUN |3 BIOCONDUCTOR_VERSION=3.14 BIOCONDUCTOR_PATCH=30 BIOCONDUCTOR_DOCKER_VERSION=3.14.30248 B
30RUN |3 BIOCONDUCTOR_VERSION=3.14 BIOCONDUCTOR_PATCH=30 BIOCONDUCTOR_DOCKER_VERSION=3.14.30212 B
31ENV DEBIAN_FRONTEND=noninteractive0 B
32RUN |3 BIOCONDUCTOR_VERSION=3.14 BIOCONDUCTOR_PATCH=30 BIOCONDUCTOR_DOCKER_VERSION=3.14.30586.99 MB
33RUN |3 BIOCONDUCTOR_VERSION=3.14 BIOCONDUCTOR_PATCH=30 BIOCONDUCTOR_DOCKER_VERSION=3.14.30192.58 MB
34RUN |3 BIOCONDUCTOR_VERSION=3.14 BIOCONDUCTOR_PATCH=30 BIOCONDUCTOR_DOCKER_VERSION=3.14.304.6 MB
35RUN |3 BIOCONDUCTOR_VERSION=3.14 BIOCONDUCTOR_PATCH=30 BIOCONDUCTOR_DOCKER_VERSION=3.14.30269 B
36ADD install.R /tmp/ # buildkit263 B
37RUN |3 BIOCONDUCTOR_VERSION=3.14 BIOCONDUCTOR_PATCH=30 BIOCONDUCTOR_DOCKER_VERSION=3.14.3034.54 MB
38RUN |3 BIOCONDUCTOR_VERSION=3.14 BIOCONDUCTOR_PATCH=30 BIOCONDUCTOR_DOCKER_VERSION=3.14.30342 B
39ENV LIBSBML_CFLAGS=-I/usr/include0 B
40ENV LIBSBML_LIBS=-lsbml0 B
41ENV BIOCONDUCTOR_DOCKER_VERSION=3.14.300 B
42ENV BIOCONDUCTOR_VERSION=3.140 B
43CMD ["/init"]0 B
44LABEL Image=for basic ad-hoc bioinformatic0 B
45RUN /bin/sh -c apt-get update99.44 MB
46ENV HTSLIB_INSTALL_DIR=/opt/htslib0 B
47WORKDIR /tmp32 B
48RUN /bin/sh -c wget https://github.com/samtools/htslib/releases/download/1.14/htslib-1.14.tar.bz214.93 MB
49WORKDIR /tmp32 B
50RUN /bin/sh -c wget https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz21.46 MB
51RUN /bin/sh -c wget https://github.com/samtools/bcftools/releases/download/1.14/bcftools-1.14.tar.bz25.17 MB
52COPY /bin/bam-readcount /opt/bam-readcount/ # buildkit2.23 MB
53COPY bam_readcount_helper.py /usr/bin/bam_readcount_helper.py # buildkit1.24 KB
54WORKDIR /opt32 B
55RUN /bin/sh -c wget https://github.com/broadinstitute/gatk/releases/download/4.2.3.0/gatk-4.2.3.0.zip882.12 MB
56ENV PATH=/opt/gatk-4.2.3.0/bin:/usr/lib/rstudio-server/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
57COPY split_interval_list_helper.pl /usr/bin/split_interval_list_helper.pl # buildkit374 B
58WORKDIR /tmp32 B
59RUN /bin/sh -c wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary13.48 MB
60WORKDIR /tmp32 B
61RUN /bin/sh -c wget https://github.com/vcftools/vcftools/releases/download/v0.1.16/vcftools-0.1.16.tar.gz6.63 MB
62RUN /bin/sh -c mkdir -p17.3 MB
63ADD rpackages.R /tmp/ # buildkit300 B
64RUN /bin/sh -c R -f186.91 MB
65RUN /bin/sh -c cd /tmp/62.96 KB
66ENV CONDA_DIR=/opt/conda0 B
67ENV PATH=/opt/conda/bin:/opt/gatk-4.2.3.0/bin:/usr/lib/rstudio-server/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
68RUN /bin/sh -c cd /tmp76.52 MB
69RUN /bin/sh -c conda install342.02 MB
70WORKDIR /opt32 B
71RUN /bin/sh -c wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip19.39 MB
72RUN /bin/sh -c ln -sf566.46 KB
73RUN /bin/sh -c dbus-uuidgen >/etc/machine-id161 B
74RUN /bin/sh -c cd /931.01 KB
75ADD utilities/* /usr/bin/ # buildkit1.48 KB

Command

ADD file:5d68d27cc15a80653c93d3a0b262a28112d47a46326ff5fc2dfbf7fa3b9a0ce8 in /