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Dockerfile
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FROM python:3.8-slim
RUN apt-get update && \
apt-get upgrade -y && \
apt-get install -y \
autoconf \
automake \
build-essential \
cmake \
libbz2-dev \
libcurl4-gnutls-dev \
liblzma-dev \
libncurses5-dev \
libssl-dev \
make \
unzip \
wget \
zlib1g-dev && \
apt-get clean && \
apt-get purge && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
WORKDIR /app
## Install samtools for cram processing
RUN wget --no-verbose https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 && \
bunzip2 samtools-1.10.tar.bz2 && \
tar -xf samtools-1.10.tar && \
cd samtools-1.10 && \
./configure && \
make all all-htslib && \
make install install-htslib && \
rm /app/samtools-1.10.tar
## Set TIDDIT version
ARG TIDDIT_VERSION=2.12.1
## Add some info
LABEL base_image="python:3.8-slim"
LABEL software="TIDDIT.py"
LABEL software.version=${TIDDIT_VERSION}
## Download and extract
RUN wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-${TIDDIT_VERSION}.zip && \
unzip TIDDIT-${TIDDIT_VERSION}.zip && \
rm TIDDIT-${TIDDIT_VERSION}.zip
## Install
RUN cd TIDDIT-TIDDIT-${TIDDIT_VERSION} && \
./INSTALL.sh && \
chmod +x /app/TIDDIT-TIDDIT-${TIDDIT_VERSION}/TIDDIT.py && \
ln -s /app/TIDDIT-TIDDIT-${TIDDIT_VERSION}/TIDDIT.py /usr/local/bin
ENTRYPOINT ["TIDDIT.py"]
CMD ["--help"]