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Dockerfile
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############################################################
# Dockerfile to build proatac
############################################################
FROM ubuntu:16.04
MAINTAINER Caleb Lareau; caleblareau@g.harvard.edu
# apt update and install global requirements
RUN apt-get clean all &&\
apt-get update &&\
apt-get upgrade -y && \
apt-get install -y -qq \
autotools-dev \
automake \
cmake \
curl \
fuse \
git \
wget \
zip \
unzip \
libtbb-dev \
openjdk-8-jdk \
build-essential \
r-base \
pkg-config \
python \
python-dev \
python-pip \
python3 \
python3-dev \
python3-pip \
zlib1g-dev \
libncurses5-dev \
libbz2-dev \
liblzma-dev \
libmagic-dev &&\
apt-get clean && \
apt-get purge && \
# Install python packages
pip install python-magic && \
pip install numpy && \
pip install wheel && \
pip install setuptools && \
pip install macs2 && \
pip3 install proatac && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/doc/*
### Installing necessary R packages
RUN Rscript -e 'install.packages("devtools", repos = "http://cran.us.r-project.org"); \
devtools::install_github("caleblareau/BuenColors")'
### Installing bowtie2
ENV VERSION 2.3.0
ENV NAME bowtie2
ENV URL "https://github.com/BenLangmead/bowtie2/archive/v${VERSION}.tar.gz"
RUN wget -q -O - $URL | tar -zxv && \
cd ${NAME}-${VERSION} && \
make -j 4 && \
cd .. && \
cp ./${NAME}-${VERSION}/${NAME} /usr/local/bin/ && \
cp ./${NAME}-${VERSION}/${NAME}-* /usr/local/bin/ && \
strip /usr/local/bin/*; true && \
rm -rf ./${NAME}-${VERSION}/
### Installing samtools/htslib/tabix/bgzip
ENV VERSIONH 1.4
ENV NAMEH htslib
ENV URLH "https://github.com/samtools/${NAMEH}/releases/download/${VERSIONH}/${NAMEH}-${VERSIONH}.tar.bz2"
ENV VERSION 1.4
ENV NAME "samtools"
ENV URL "https://github.com/samtools/${NAME}/releases/download/${VERSION}/${NAME}-${VERSION}.tar.bz2"
RUN wget -q $URLH && \
bzip2 -d ${NAMEH}-${VERSIONH}.tar.bz2 && \
tar -xf ${NAMEH}-${VERSIONH}.tar && \
cd ${NAMEH}-${VERSIONH} && \
./configure && \
make -j 4 && \
cd .. && \
cp ./${NAMEH}-${VERSIONH}/tabix /usr/local/bin/ && \
cp ./${NAMEH}-${VERSIONH}/bgzip /usr/local/bin/ && \
cp ./${NAMEH}-${VERSIONH}/htsfile /usr/local/bin/ && \
strip /usr/local/bin/tabix; true && \
strip /usr/local/bin/bgzip; true && \
strip /usr/local/bin/htsfile; true && \
wget -q $URL && \
bzip2 -d ${NAME}-${VERSION}.tar.bz2 && \
tar -xf ${NAME}-${VERSION}.tar && \
cd ${NAME}-${VERSION} && \
./configure && \
make -j 4 && \
cd .. && \
cp ./${NAME}-${VERSION}/${NAME} /usr/local/bin/ && \
strip /usr/local/bin/${NAME}; true && \
rm -rf ./${NAME}-${VERSION}/ && \
rm -rf ./${NAME}-${VERSION}.tar && \
rm -rf ./${NAMEH}-${VERSIONH}/ && \
rm -rf ./${NAMEH}-${VERSIONH}.tar
### Installing bedtools
ENV VERSION 2.26.0
ENV NAME bedtools2
ENV URL "https://github.com/arq5x/bedtools2/releases/download/v${VERSION}/bedtools-${VERSION}.tar.gz"
RUN wget -q -O - $URL | tar -zxv && \
cd ${NAME} && \
make -j 4 && \
cd .. && \
cp ./${NAME}/bin/bedtools /usr/local/bin/ && \
strip /usr/local/bin/*; true && \
rm -rf ./${NAME}/
# Shouldn't need to update the working directory or copy anything. Maybe do a test like in Ariadne