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Dockerfile
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FROM ubuntu:latest
LABEL description="cosigt"
LABEL base_image="ubuntu:latest"
LABEL software="cosigt"
LABEL about.home="https://github.com/davidebolo1993/cosigt"
LABEL about.license="GPLv3"
ARG DEBIAN_FRONTEND=noninteractive
#install basic libraries and python
#this is useful for having control on all the depenendencies
#odgi and pggb are excluded here
WORKDIR /opt
RUN apt-get update
RUN apt-get -y install build-essential \
software-properties-common \
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 \
pigz \
clang-14 \
libomp5 libomp-dev libssl-dev libssl3 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 \
&& rm -rf /var/cache
#install rust
RUN curl https://sh.rustup.rs -sSf | sh -s -- -y
ENV PATH="/root/.cargo/bin:${PATH}"
#and update
RUN rustup update
RUN cargo install --locked maturin
#install numpy
RUN pip3 install numpy \
pandas \
matplotlib \
scikit-learn \
scipy \
pyfaidx \
--break-system-packages
#ln python to python3 -not used right now but, who knows?
RUN ln -s /usr/bin/python3 /usr/bin/python
##install samtools
RUN wget https://github.com/samtools/samtools/releases/download/1.19.2/samtools-1.19.2.tar.bz2 \
&& tar -jxvf samtools-1.19.2.tar.bz2 \
&& rm samtools-1.19.2.tar.bz2 \
&& cd samtools-1.19.2 \
&& ./configure \
&& make \
&& make install
##install bwa-mem
RUN git clone https://github.com/lh3/bwa.git \
&& cd bwa \
&& git checkout 79b230de48c74156f9d3c26795a360fc5a2d5d3b \
&& make
ENV PATH /opt/bwa:$PATH
##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
ENV PATH /opt:$PATH
##install gafpack
RUN git clone https://github.com/ekg/gafpack.git \
&& cd gafpack \
&& git checkout cf2e96057c4efe86317caa990b53f1fc1fdc6367 \
&& cargo install --force --path .
ENV PATH /opt/gafpack/target/release:$PATH
##install gfainject
RUN git clone https://github.com/chfi/gfainject.git \
&& cd gfainject \
&& git checkout e56cba362047e7137352858dfba5f56e944cbf06 \
&& cargo install --force --path .
ENV PATH /opt/gfainject/target/release:$PATH
##install impg
RUN git clone https://github.com/pangenome/impg \
&& cd impg \
&& git checkout 4cf6009160ec9d64e9f9972248511a63d6d012a5 \
&& cargo install --force --path .
ENV PATH /opt/impg/target/release:$PATH
##install cosigt
RUN git clone https://github.com/davidebolo1993/cosigt.git \
&& cd cosigt \
&& go mod init cosigt \
&& go mod tidy \
&& go build cosigt
ENV PATH /opt/cosigt:$PATH