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pgkb/pharmcat:2.13.0

Multi-platform
Machine learning & AI
Data science
Index digest

sha256:5a3483eea127e5e29af6f69879a597be7bcacdb3f42b2704ceebc4a4daf488e2

OS/ARCH

Compressed size

1.63 GB

Last pushed

over 2 years by pharmgen

Type

Image

Manifest digest

sha256:d4e0b8c236c71b9590f87520cfe5cd445fde51fd7c7ae79836170f8a6f4e022d

Image Layers

Image Layers

1ADD file ... in / 47.28 MB
2CMD ["bash"]0 B
3/bin/sh -c set -eux; apt-get22.94 MB
4/bin/sh -c set -eux; apt-get61.17 MB
5/bin/sh -c set -ex; apt-get201.42 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;6.1 MB
9ENV GPG_KEY=7169605F62C751356D054A26A821E680E5FA63050 B
10ENV PYTHON_VERSION=3.12.40 B
11RUN /bin/sh -c set -eux;21.66 MB
12RUN /bin/sh -c set -eux;245 B
13ENV PYTHON_PIP_VERSION=24.00 B
14ENV PYTHON_GET_PIP_URL=https://github.com/pypa/get-pip/raw/dbf0c85f76fb6e1ab42aa672ffca6f0a675d9ee4/public/get-pip.py0 B
15ENV PYTHON_GET_PIP_SHA256=dfe9fd5c28dc98b5ac17979a953ea550cec37ae1b47a5116007395bfacff2ab90 B
16RUN /bin/sh -c set -eux;2.61 MB
17CMD ["python3"]0 B
18RUN /bin/sh -c apt-get update14.92 MB
19RUN /bin/sh -c wget -O1.7 KB
20RUN /bin/sh -c echo "deb227 B
21RUN /bin/sh -c apt-get update185.99 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-${HTSLIB_VERSION}/20.58 KB
37RUN /bin/sh -c cd /usr/local/bin/htslib-${HTSLIB_VERSION}/69.24 MB
38RUN /bin/sh -c cd /usr/local/bin/bcftools-${BCFTOOLS_VERSION}/33.98 KB
39RUN /bin/sh -c cd /usr/local/bin/bcftools-${BCFTOOLS_VERSION}/20.51 MB
40RUN /bin/sh -c cd /usr/local/bin/samtools-${SAMTOOLS_VERSION}/34.35 KB
41RUN /bin/sh -c cd /usr/local/bin/samtools-${SAMTOOLS_VERSION}/28.89 MB
42RUN /bin/sh -c rm 184 B
43RUN /bin/sh -c rm -rf178 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 -rf178 B
48COPY preprocessor/requirements.txt ./ # buildkit233 B
49RUN /bin/sh -c pip3 install76.98 MB
50RUN /bin/sh -c rm requirements.txt182 B
51COPY src/main/config/bashrc /root/.bashrc # buildkit504 B
52WORKDIR /pharmcat32 B
53COPY preprocessor/pharmcat_vcf_preprocessor.py preprocessor/pharmcat_pipeline bin/pharmcat build/pharmcat.jar27.03 MB
54RUN /bin/sh -c mkdir preprocessor126 B
55COPY preprocessor/preprocessor/*.py preprocessor/preprocessor/*.tsv preprocessor/ #14.92 KB
56RUN /bin/sh -c mkdir data116 B
57RUN /bin/sh -c chmod 7555.6 KB
58RUN /bin/sh -c python -c72.81 KB

Command

ADD file:b9a9fc37b874060c713002ae1ac220f097edd7c6576116c22bb15aad8229b1b3 in /