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pgkb/pharmcat:2.14.0

Multi-platform
Machine learning & AI
Data science
Index digest

sha256:8f1564c72c3367ed11c915918f21bea5bf3d85783f675efb239d6cc9bd34ded4

OS/ARCH

Compressed size

1.61 GB

Last pushed

about 2 years by pharmgen

Type

Image

Manifest digest

sha256:d2ecca81eb3743237df46b09d5e5db7a9af33811f9b3c65407fd45a4cc9b69b9

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-get193.22 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=3.12.40 B
11RUN /bin/sh -c set -eux;21.2 MB
12RUN /bin/sh -c set -eux;233 B
13ENV PYTHON_PIP_VERSION=24.00 B
14ENV PYTHON_GET_PIP_URL=https://github.com/pypa/get-pip/raw/e03e1607ad60522cf34a92e834138eb89f57667c/public/get-pip.py0 B
15ENV PYTHON_GET_PIP_SHA256=ee09098395e42eb1f82ef4acb231a767a6ae85504a9cf9983223df0a7cbd35d70 B
16RUN /bin/sh -c set -eux;2.67 MB
17CMD ["python3"]0 B
18RUN /bin/sh -c apt-get update18.11 MB
19RUN /bin/sh -c wget -O1.7 KB
20RUN /bin/sh -c echo "deb226 B
21RUN /bin/sh -c apt-get update184.81 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-${BCFTOOLS_VERSION}/32.43 KB
39RUN /bin/sh -c cd /usr/local/bin/bcftools-${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 184 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 185 B
47RUN /bin/sh -c rm -rf177 B
48COPY preprocessor/requirements.txt ./ # buildkit232 B
49RUN /bin/sh -c pip3 install73.4 MB
50RUN /bin/sh -c rm requirements.txt182 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.jar27.04 MB
54RUN /bin/sh -c mkdir preprocessor125 B
55COPY preprocessor/preprocessor/*.py preprocessor/preprocessor/*.tsv preprocessor/ #14.91 KB
56RUN /bin/sh -c mkdir data118 B
57RUN /bin/sh -c chmod 7555.6 KB
58RUN /bin/sh -c python -c72.81 KB

Command

ADD file:696648070a57689a69a184fda234045f7be4a8a9f3b2fff9031ff0a2d9914113 in /