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pgkb/pharmcat:2.10.0

Machine learning & AI
Data science
Index digest

sha256:c8d1266f3d67a02859a4cc04aa517df90daff4dc63642c6a29cf18903aa6b58b

OS/ARCH

linux/amd64

Compressed size

1.62 GB

Last pushed

over 2 years by pharmgen

Type

Image

Manifest digest

sha256:5a1bb69b401b5ddbf799d5bbb21d3d1f66514d421ef31b8e73db6fb5bfdd50d2

Image Layers

Image Layers

1ADD file ... in / 47.26 MB
2CMD ["bash"]0 B
3/bin/sh -c set -eux; apt-get22.93 MB
4/bin/sh -c set -eux; apt-get61.17 MB
5/bin/sh -c set -ex; apt-get201.36 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;6.09 MB
9ENV GPG_KEY=E3FF2839C048B25C084DEBE9B26995E3102505680 B
10ENV PYTHON_VERSION=3.10.140 B
11RUN /bin/sh -c set -eux;16.36 MB
12RUN /bin/sh -c set -eux;242 B
13ENV PYTHON_PIP_VERSION=23.0.10 B
14ENV PYTHON_SETUPTOOLS_VERSION=65.5.10 B
15ENV PYTHON_GET_PIP_URL=https://github.com/pypa/get-pip/raw/dbf0c85f76fb6e1ab42aa672ffca6f0a675d9ee4/public/get-pip.py0 B
16ENV PYTHON_GET_PIP_SHA256=dfe9fd5c28dc98b5ac17979a953ea550cec37ae1b47a5116007395bfacff2ab90 B
17RUN /bin/sh -c set -eux;2.94 MB
18CMD ["python3"]0 B
19RUN /bin/sh -c apt-get update14.9 MB
20RUN /bin/sh -c wget -O1.71 KB
21RUN /bin/sh -c echo "deb225 B
22RUN /bin/sh -c apt-get update185.8 MB
23RUN /bin/sh -c mkdir /pharmcat98 B
24WORKDIR /pharmcat32 B
25RUN /bin/sh -c wget https://zenodo.org/record/7288118/files/GRCh38_reference_fasta.tar842.05 MB
26ENV BCFTOOLS_VERSION=1.180 B
27ENV HTSLIB_VERSION=1.180 B
28ENV SAMTOOLS_VERSION=1.180 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.bz24.53 MB
31RUN /bin/sh -c wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz27.37 MB
32RUN /bin/sh -c wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz28.65 MB
33RUN /bin/sh -c tar -xjf4.63 MB
34RUN /bin/sh -c tar -xjf7.99 MB
35RUN /bin/sh -c tar -xjf9.99 MB
36RUN /bin/sh -c cd /usr/local/bin/htslib-${HTSLIB_VERSION}/20.52 KB
37RUN /bin/sh -c cd /usr/local/bin/htslib-${HTSLIB_VERSION}/64.23 MB
38RUN /bin/sh -c cd /usr/local/bin/bcftools-${BCFTOOLS_VERSION}/33.87 KB
39RUN /bin/sh -c cd /usr/local/bin/bcftools-${BCFTOOLS_VERSION}/19.91 MB
40RUN /bin/sh -c cd /usr/local/bin/samtools-${SAMTOOLS_VERSION}/34.23 KB
41RUN /bin/sh -c cd /usr/local/bin/samtools-${SAMTOOLS_VERSION}/28.3 MB
42RUN /bin/sh -c rm 188 B
43RUN /bin/sh -c rm -rf181 B
44RUN /bin/sh -c rm 185 B
45RUN /bin/sh -c rm -rf180 B
46RUN /bin/sh -c rm 186 B
47RUN /bin/sh -c rm -rf179 B
48COPY preprocessor/requirements.txt ./ # buildkit245 B
49RUN /bin/sh -c pip3 install94.63 MB
50RUN /bin/sh -c rm requirements.txt183 B
51COPY src/main/config/bashrc /root/.bashrc # buildkit505 B
52WORKDIR /pharmcat32 B
53COPY preprocessor/pharmcat_vcf_preprocessor.py preprocessor/pharmcat_pipeline bin/pharmcat build/pharmcat.jar9.48 MB
54RUN /bin/sh -c mkdir preprocessor124 B
55COPY preprocessor/preprocessor/*.py preprocessor/preprocessor/*.tsv preprocessor/ #14.27 KB
56RUN /bin/sh -c mkdir data118 B
57RUN /bin/sh -c chmod 7555.21 KB
58RUN /bin/sh -c python -c103.85 KB

Command

ADD file:b18b4c32dd8042f45097997c732dc29b3917fd7d5f337f9e772eee5875fbe6f1 in /