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Dockerfile
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FROM ubuntu:22.04
MAINTAINER Mikhail Kolmogorov, [email protected]
# update and install dependencies
RUN apt-get update && \
DEBIAN_FRONTEND="noninteractive" apt-get -y install tzdata && \
apt-get -y install cmake git make gcc g++ autoconf bzip2 lzma-dev zlib1g-dev tabix libbz2-dev && \
apt-get -y install libcurl4-openssl-dev libpthread-stubs0-dev liblzma-dev libhdf5-dev && \
apt-get -y install python3-pip python3-virtualenv virtualenv python3-dev && \
apt-get -y install wget libz-dev libncurses5-dev libgsl-dev && \
apt-get -y install graphviz libgraphviz-dev pkg-config && \
apt-get clean && \
apt-get purge && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN ln -s /usr/bin/python3 /usr/bin/python
RUN python3 --version && \
python3 -m pip install --upgrade pip
ARG MM_VER=2.28
RUN wget https://github.com/lh3/minimap2/releases/download/v$MM_VER/minimap2-$MM_VER.tar.bz2 && \
tar xvf minimap2-$MM_VER.tar.bz2 && \
rm minimap2-$MM_VER.tar.bz2 && \
cd minimap2-$MM_VER && \
make && \
cp minimap2 /usr/bin/
### samtools
# 1.15
WORKDIR /opt/samtools
RUN wget https://github.com/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2 && \
tar xvf samtools-1.15.tar.bz2 && \
rm -r /opt/samtools/samtools-1.15.tar.bz2 && \
cd samtools-1.15/ && \
autoheader && \
autoconf -Wno-header && \
./configure && \
make && \
cp samtools /usr/bin/samtools
### bcftools
WORKDIR /opt/bcftools
RUN wget https://github.com/samtools/bcftools/releases/download/1.15/bcftools-1.15.tar.bz2 && \
tar xvf bcftools-1.15.tar.bz2 && \
cd bcftools-1.15/ && \
autoheader && \
autoconf -Wno-header && \
./configure --enable-libgsl && \
make && \
cp bcftools /usr/bin/bcftools
#build and install Flye
WORKDIR /opt/flye
RUN git clone https://github.com/fenderglass/Flye && \
cd Flye && \
python setup.py install
#Install strainy & dependencies
WORKDIR /opt/strainy
RUN git clone -b docker https://github.com/katerinakazantseva/strainy && \
cd strainy && \
python3 -m pip install -r requirements.txt && \
python3 setup.py install
ENV PYTHONUNBUFFERED "1"