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Last active February 6, 2023 19:44
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a Dockerfile for HTSLib, SAM Tools, BCF Tools, Plink-2.0 and Python with more on the way.
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Dockerfile
# SOURCE AND CREDITS: https://github.com/chrishah/samtools-docker/blob/master/Dockerfile
FROM alpine:latest
LABEL version="v1.0" description="A docekr image for the Pharmacogenetics ANalysis Pipeline" maintainer="Graeme Ford <Graeme.Ford@tuks.co.za>"
RUN apk update && apk upgrade
# Install python/pip
ENV PYTHONUNBUFFERED=1
RUN apk add --update --no-cache python3 && ln -sf python3 /usr/bin/python
RUN python3 -m ensurepip
RUN pip3 install --no-cache --upgrade pip setuptools
RUN apk add --no-cache build-base
RUN apk add --no-cache ncurses-dev
RUN apk add --no-cache zlib-dev
RUN apk add --no-cache bzip2-dev
RUN apk add --no-cache xz-dev
RUN apk add --no-cache curl
WORKDIR /tmp
#Samtools
ENV SAMTOOLS_INSTALL_DIR=/opt/samtools
ENV SAMTOOLS_VERSION=1.16.1
RUN wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2 && \
tar --bzip2 -xf samtools-$SAMTOOLS_VERSION.tar.bz2
WORKDIR /tmp/samtools-$SAMTOOLS_VERSION
RUN ./configure --prefix=/usr/ && \
make && \
make install
# BCFTools
WORKDIR /tmp
ENV BCFTOOLS_VERSION=1.16
RUN wget https://github.com/samtools/bcftools/releases/download/$BCFTOOLS_VERSION/bcftools-$BCFTOOLS_VERSION.tar.bz2 && \
tar --bzip2 -xf bcftools-$BCFTOOLS_VERSION.tar.bz2
WORKDIR /tmp/bcftools-$BCFTOOLS_VERSION
RUN ./configure -prefix=/usr/ && \
make && \
make install
# HTSLib
WORKDIR /tmp
ENV HTSLIB_VERSION=1.16
RUN wget https://github.com/samtools/htslib/releases/download/$HTSLIB_VERSION/htslib-$HTSLIB_VERSION.tar.bz2 && \
tar --bzip2 -xf htslib-$HTSLIB_VERSION.tar.bz2
WORKDIR /tmp/htslib-$HTSLIB_VERSION
RUN ./configure -prefix=/usr/ && \
make && \
make install
WORKDIR /work
# Plink-2.0
RUN wget https://s3.amazonaws.com/plink2-assets/alpha3/plink2_linux_x86_64_20221024.zip
RUN unzip plink2_linux_x86_64_20221024.zip
RUN mv plink2 /usr/bin/
ENV PATH="${PATH}:/usr/bin/"
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