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pgkb/pharmcat-tutorial:latest

Machine learning & AI
Data science
Manifest digest

sha256:05b7343225ee27e1708568f498905b3c83603ae4526fa5c41f29dbb8de84eb79

OS/ARCH

linux/amd64

Compressed size

2.39 GB

Last pushed

almost 4 years by pharmgen

Type

Image

Manifest digest

sha256:05b7343225ee27e1708568f498905b3c83603ae4526fa5c41f29dbb8de84eb79

Image Layers

Image Layers

1ADD file ... in / 52.5 MB
2CMD ["bash"]0 B
3/bin/sh -c set -eux; apt-get4.93 MB
4/bin/sh -c set -ex; if10.37 MB
5/bin/sh -c apt-get update &&52.06 MB
6/bin/sh -c set -ex; apt-get187.75 MB
7ENV PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
8ENV LANG=C.UTF-80 B
9/bin/sh -c set -eux; apt-get6 MB
10ENV GPG_KEY=A035C8C19219BA821ECEA86B64E628F8D684696D0 B
11ENV PYTHON_VERSION=3.10.80 B
12/bin/sh -c set -eux; wget19.11 MB
13/bin/sh -c set -eux; for233 B
14ENV PYTHON_PIP_VERSION=22.2.20 B
15ENV PYTHON_SETUPTOOLS_VERSION=63.2.00 B
16ENV PYTHON_GET_PIP_URL=https://github.com/pypa/get-pip/raw/6d265be7a6b5bc4e9c5c07646aee0bf0394be03d/public/get-pip.py0 B
17ENV PYTHON_GET_PIP_SHA256=36c6f6214694ef64cc70f4127ac0ccec668408a93825359d998fb31d24968d670 B
18/bin/sh -c set -eux; wget2.9 MB
19CMD ["python3"]0 B
20RUN /bin/sh -c apt-get update17.25 MB
21RUN /bin/sh -c wget -O1.71 KB
22RUN /bin/sh -c echo "deb230 B
23RUN /bin/sh -c apt-get update185.08 MB
24RUN /bin/sh -c mkdir /pharmcat101 B
25WORKDIR /pharmcat32 B
26RUN /bin/sh -c wget https://zenodo.org/record/7288118/files/GRCh38_reference_fasta.tar842.05 MB
27ENV BCFTOOLS_VERSION=1.160 B
28ENV HTSLIB_VERSION=1.160 B
29ENV SAMTOOLS_VERSION=1.160 B
30WORKDIR /usr/local/bin/32 B
31RUN /bin/sh -c wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz24.26 MB
32RUN /bin/sh -c wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz26.98 MB
33RUN /bin/sh -c wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz27.81 MB
34RUN /bin/sh -c tar -xjf4.43 MB
35RUN /bin/sh -c tar -xjf7.7 MB
36RUN /bin/sh -c tar -xjf9.18 MB
37RUN /bin/sh -c cd /usr/local/bin/htslib-${HTSLIB_VERSION}/18.98 KB
38RUN /bin/sh -c cd /usr/local/bin/htslib-${HTSLIB_VERSION}/62.99 MB
39RUN /bin/sh -c cd /usr/local/bin/bcftools-${BCFTOOLS_VERSION}/32.67 KB
40RUN /bin/sh -c cd /usr/local/bin/bcftools-${BCFTOOLS_VERSION}/19.54 MB
41RUN /bin/sh -c cd /usr/local/bin/samtools-${SAMTOOLS_VERSION}/32.71 KB
42RUN /bin/sh -c cd /usr/local/bin/samtools-${SAMTOOLS_VERSION}/28.09 MB
43RUN /bin/sh -c rm 196 B
44RUN /bin/sh -c rm -rf189 B
45RUN /bin/sh -c rm 194 B
46RUN /bin/sh -c rm -rf188 B
47RUN /bin/sh -c rm 196 B
48RUN /bin/sh -c rm -rf189 B
49COPY src/scripts/preprocessor/requirements.txt ./ # buildkit222 B
50RUN /bin/sh -c pip3 install115.36 MB
51RUN /bin/sh -c rm requirements.txt193 B
52COPY src/main/config/bashrc /root/.bashrc # buildkit490 B
53WORKDIR /pharmcat32 B
54COPY src/scripts/preprocessor/pharmcat_vcf_preprocessor.py bin/pharmcat build/pharmcat.jar pharmcat_positions.vcf*8.68 MB
55RUN /bin/sh -c mkdir preprocessor133 B
56COPY src/scripts/preprocessor/preprocessor/*.py src/scripts/preprocessor/preprocessor/*.tsv preprocessor/ #11.87 KB
57RUN /bin/sh -c mkdir data125 B
58RUN /bin/sh -c chmod 7553 KB
59RUN /bin/sh -c python -c87.87 KB
60RUN /bin/sh -c apt install174.87 MB
61RUN /bin/sh -c R -e214.87 KB
62RUN /bin/sh -c R -e22.4 MB
63RUN /bin/sh -c R -e71.1 MB
64RUN /bin/sh -c R -e818.04 KB
65RUN /bin/sh -c R -e30.46 MB
66RUN /bin/sh -c git clone434.62 MB
67RUN /bin/sh -c mv PharmCAT-tutorial/*56.39 MB
68WORKDIR /pharmcat/32 B

Command

ADD file:26702ba2c3e94cb21cdb3c550cf01cf848823d160f3417b559116d4c718e5df0 in /