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Dockerfile
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FROM ubuntu:20.04
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update && apt-get install -y --no-install-recommends \
build-essential unzip wget openjdk-11-jre time locales \
make python3-pip \
python3-dev \
cpanminus bwa \
libncurses5-dev libbz2-dev liblzma-dev python \
bc parallel meson ninja-build libvcflib-tools vcftools zlib1g pkg-config cmake
WORKDIR /usr/local/
RUN wget 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip' && \
unzip fastqc_v0.11.5.zip && \
rm fastqc_v0.11.5.zip && \
cd FastQC && \
chmod 755 fastqc && \
ln -s /usr/local/FastQC/fastqc /usr/local/bin/fastqc
RUN pip install multiqc
ENV LC_ALL C
ENV PATH=/usr/local/bin:$PATH
# samtools
ARG SAMTOOLSVER=1.16.1
RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLSVER}/samtools-${SAMTOOLSVER}.tar.bz2 && \
tar -xjf samtools-${SAMTOOLSVER}.tar.bz2 && \
rm samtools-${SAMTOOLSVER}.tar.bz2 && \
cd samtools-${SAMTOOLSVER} && \
./configure && \
make && \
make install && rm -rf /usr/local/samtools-${SAMTOOLSVER}
#bcftools
ARG BCFTOOLSVER=1.16
RUN wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLSVER}/bcftools-${BCFTOOLSVER}.tar.bz2 && \
tar -xjf bcftools-${BCFTOOLSVER}.tar.bz2 && \
rm bcftools-${BCFTOOLSVER}.tar.bz2 && \
cd bcftools-${BCFTOOLSVER} && \
./configure && \
make && \
make install && rm -rf /usr/local/bcftools-${BCFTOOLSVER}
# GATK
RUN wget 'https://github.com/broadinstitute/gatk/releases/download/4.3.0.0/gatk-4.3.0.0.zip' && \
unzip gatk-4.3.0.0.zip && rm gatk-4.3.0.0.zip
ENV PATH=/usr/local/gatk-4.3.0.0/:${PATH}
RUN wget 'https://github.com/freebayes/freebayes/releases/download/v1.3.6/freebayes-1.3.6-src.tar.gz' && \
tar -zxvf freebayes-1.3.6-src.tar.gz && \
cd freebayes && \
meson build/ --buildtype release && \
cd build && ninja && rm /usr/local/freebayes-1.3.6-src.tar.gz
ENV PATH=/usr/local/freebayes/build/:/usr/local/freebayes/scripts/:${PATH}
# Fastp
WORKDIR /usr/local/bin/
RUN wget http://opengene.org/fastp/fastp.0.23.1 && \
mv fastp.0.23.1 fastp &&\
chmod a+x ./fastp
#htslib
ARG HTSLIBVER=1.16
RUN wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 && \
tar -xjf htslib-${HTSLIBVER}.tar.bz2 && \
rm htslib-${HTSLIBVER}.tar.bz2 && \
cd htslib-${HTSLIBVER} && \
./configure && \
make && \
make install && rm -rf /usr/local/htslib-${HTSLIBVER}
#
# ------ Installing vcflib / vcfwave. Installs but vcfwave seems buggy as of 24Feb 2023 ----- #
#
# RUN apt-get update && apt-get install -y --no-install-recommends \
# git cmake libhts-dev libtabixpp-dev libtabixpp0 \
# pybind11-dev libcurl4-openssl-dev python-dev \
# libomp-dev
# WORKDIR /usr/local/
# RUN git clone --recursive https://github.com/vcflib/vcflib.git && \
# cd vcflib && \
# mkdir -p build && cd build && \
# cmake -DCMAKE_BUILD_TYPE=Release -DZIG=OFF .. && \
# cmake --build . && \
# cmake --install .
#ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/vcflib/build/contrib/WFA2-lib/
# Cleanup apt package lists to save space
RUN rm -rf /var/lib/apt/lists/*