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pgkb/pharmcat:2.15.2

Multi-platform
Machine learning & AI
Data science
Index digest

sha256:10d92b712e7ecf03f2a77f6e19a0e657f3f42cbdaad1733f84ed9fa92392da00

OS/ARCH

Compressed size

1.61 GB

Last pushed

about 2 years by pharmgen

Type

Image

Manifest digest

sha256:2a3e4e85a9e232414fe66f079fbe1d72e196ed3243a219b09af72f3d0310ee86

Image Layers

Image Layers

1ADD file ... in / 47.29 MB
2CMD ["bash"]0 B
3/bin/sh -c set -eux; apt-get22.5 MB
4/bin/sh -c set -eux; apt-get61.03 MB
5/bin/sh -c set -ex; apt-get193.24 MB
6ENV PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
7ENV LANG=C.UTF-80 B
8RUN /bin/sh -c set -eux;5.95 MB
9ENV GPG_KEY=7169605F62C751356D054A26A821E680E5FA63050 B
10ENV PYTHON_VERSION=3.12.50 B
11RUN /bin/sh -c set -eux;20.94 MB
12RUN /bin/sh -c set -eux;232 B
13ENV PYTHON_PIP_VERSION=24.20 B
14ENV PYTHON_GET_PIP_URL=https://github.com/pypa/get-pip/raw/66d8a0f637083e2c3ddffc0cb1e65ce126afb856/public/get-pip.py0 B
15ENV PYTHON_GET_PIP_SHA256=6fb7b781206356f45ad79efbb19322caa6c2a5ad39092d0d44d0fec94117e1180 B
16RUN /bin/sh -c set -eux;3.72 MB
17CMD ["python3"]0 B
18RUN /bin/sh -c apt-get update14.78 MB
19RUN /bin/sh -c wget -qO1.72 KB
20RUN /bin/sh -c echo "deb229 B
21RUN /bin/sh -c apt-get update184.89 MB
22RUN /bin/sh -c mkdir /pharmcat98 B
23WORKDIR /pharmcat32 B
24ENV PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/pharmcat0 B
25RUN /bin/sh -c wget https://zenodo.org/record/7288118/files/GRCh38_reference_fasta.tar842.05 MB
26ENV BCFTOOLS_VERSION=1.200 B
27ENV HTSLIB_VERSION=1.200 B
28ENV SAMTOOLS_VERSION=1.200 B
29WORKDIR /usr/local/bin/32 B
30RUN /bin/sh -c wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz24.56 MB
31RUN /bin/sh -c wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz27.51 MB
32RUN /bin/sh -c wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz28.73 MB
33RUN /bin/sh -c tar -xjf4.7 MB
34RUN /bin/sh -c tar -xjf8.16 MB
35RUN /bin/sh -c tar -xjf10.09 MB
36RUN /bin/sh -c cd /usr/local/bin/htslib-${HTSLIB_VERSION}/19.22 KB
37RUN /bin/sh -c cd /usr/local/bin/htslib-${HTSLIB_VERSION}/62.84 MB
38RUN /bin/sh -c cd /usr/local/bin/bcftools-${BCFTOOLS_VERSION}/32.44 KB
39RUN /bin/sh -c cd /usr/local/bin/bcftools-${BCFTOOLS_VERSION}/19.28 MB
40RUN /bin/sh -c cd /usr/local/bin/samtools-${SAMTOOLS_VERSION}/32.8 KB
41RUN /bin/sh -c cd /usr/local/bin/samtools-${SAMTOOLS_VERSION}/26.58 MB
42RUN /bin/sh -c rm 185 B
43RUN /bin/sh -c rm -rf179 B
44RUN /bin/sh -c rm 183 B
45RUN /bin/sh -c rm -rf176 B
46RUN /bin/sh -c rm 184 B
47RUN /bin/sh -c rm -rf179 B
48COPY preprocessor/requirements.txt ./ # buildkit233 B
49RUN /bin/sh -c pip3 install73.09 MB
50RUN /bin/sh -c rm requirements.txt181 B
51COPY src/main/config/bashrc /root/.bashrc # buildkit506 B
52WORKDIR /pharmcat32 B
53COPY preprocessor/pharmcat_vcf_preprocessor.py preprocessor/pharmcat_pipeline bin/pharmcat build/pharmcat.jar26.54 MB
54RUN /bin/sh -c mkdir preprocessor124 B
55COPY preprocessor/preprocessor/*.py preprocessor/preprocessor/*.tsv preprocessor/ #14.92 KB
56RUN /bin/sh -c mkdir data117 B
57RUN /bin/sh -c chmod 7555.66 KB
58RUN /bin/sh -c python -c96.59 KB

Command

ADD file:e81dd8b32e45ea6e761021a3e01b6efd339dd9248a2036dc4b51a2c1de560b4c in /