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Dockerfile
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FROM debian:bullseye-slim AS binary
LABEL description="cosigt"
LABEL base_image="debian:bullseye-slim"
LABEL software="cosigt"
LABEL about.home="https://github.com/davidebolo1993/cosigt"
LABEL about.license="GPLv3"
ARG DEBIAN_FRONTEND=noninteractive
#install basic libraries and python
WORKDIR /opt
RUN apt-get update
RUN apt-get -y install \
build-essential \
software-properties-common \
bash \
wget \
curl \
git \
bzip2 \
libbz2-dev \
zlib1g \
zlib1g-dev \
liblzma-dev \
libssl-dev \
libncurses5-dev \
libz-dev \
python3-dev \
python3-pip \
libjemalloc-dev \
cmake \
make \
g++ \
libhts-dev \
libzstd-dev \
autoconf \
libatomic-ops-dev \
pkg-config \
libomp5 \
libomp-dev \
libssl-dev \
pkg-config \
zip \
unzip
#install golang
RUN add-apt-repository ppa:longsleep/golang-backports
RUN apt-get -y install golang-go \
&& apt-get -y clean all \
&& apt-get -y purge \
&& rm -rf /var/cache \
&& rm -rf /var/lib/apt/lists/*
#install rust
RUN curl https://sh.rustup.rs -sSf | sh -s -- -y
ENV PATH="/root/.cargo/bin:${PATH}"
#and update
RUN rustup update
RUN cargo install --locked maturin
#install numpy
RUN pip3 install numpy \
pandas \
matplotlib \
scikit-learn \
scipy \
pyfaidx
#ln python to python3 -not used right now but, who knows?
RUN ln -s /usr/bin/python3 /usr/bin/python
##install samtools
RUN wget https://github.com/samtools/samtools/releases/download/1.21/samtools-1.21.tar.bz2 \
&& tar -jxvf samtools-1.21.tar.bz2 \
&& rm samtools-1.21.tar.bz2 \
&& cd samtools-1.21 \
&& ./configure \
&& make \
&& cp samtools /opt/samtools \
&& cd .. \
&& rm -rf samtools-1.21
##install bwa-mem
RUN git clone https://github.com/lh3/bwa.git \
&& cd bwa \
&& git checkout 79b230de48c74156f9d3c26795a360fc5a2d5d3b \
&& make \
&& cp bwa ../bwa-tmp \
&& cd .. \
&& rm -rf bwa \
&& mv bwa-tmp bwa
##install bwa-mem2
RUN wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2 \
&& tar -jxvf bwa-mem2-2.2.1_x64-linux.tar.bz2 \
&& rm bwa-mem2-2.2.1_x64-linux.tar.bz2
ENV PATH /opt/bwa-mem2-2.2.1_x64-linux:$PATH
##install minimap2
RUN wget https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 \
&& tar -jxvf minimap2-2.28_x64-linux.tar.bz2 \
&& rm minimap2-2.28_x64-linux.tar.bz2
ENV PATH /opt/minimap2-2.28_x64-linux:$PATH
##install bedtools
RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static \
&& chmod +x bedtools.static \
&& mv bedtools.static bedtools
## install megadepth
RUN wget https://github.com/ChristopherWilks/megadepth/releases/download/1.2.0/megadepth \
&& chmod +x megadepth
##install wfmash
RUN wget https://github.com/waveygang/wfmash/releases/download/v0.15.0/wfmash \
&& chmod +x wfmash
##install gafpack
RUN git clone https://github.com/ekg/gafpack.git \
&& cd gafpack \
&& git checkout cf2e96057c4efe86317caa990b53f1fc1fdc6367 \
&& cargo install --force --path . \
&& cp target/release/gafpack ../gafpack-tmp \
&& cd .. \
&& rm -rf gafpack \
&& mv gafpack-tmp gafpack
##install gfainject
RUN git clone https://github.com/chfi/gfainject.git \
&& cd gfainject \
&& git checkout e56cba362047e7137352858dfba5f56e944cbf06 \
&& cargo install --force --path . \
&& cp target/release/gfainject ../gfainject-tmp \
&& cd .. \
&& rm -rf gfainject \
&& mv gfainject-tmp gfainject
##install impg
RUN git clone https://github.com/pangenome/impg \
&& cd impg \
&& git checkout 4cf6009160ec9d64e9f9972248511a63d6d012a5 \
&& cargo install --force --path . \
&& cp target/release/impg ../impg-tmp \
&& cd .. \
&& rm -rf impg \
&& mv impg-tmp impg
##install cosigt
RUN git clone https://github.com/davidebolo1993/cosigt.git \
&& cd cosigt \
&& go mod init cosigt \
&& go mod tidy \
&& go build cosigt \
&& cp cosigt ../cosigt-tmp \
&& cd .. \
&& rm -rf cosigt \
&& mv cosigt-tmp cosigt
ENV PATH /opt:$PATH