ACE/Dockerfile at master · bmajoros/ACE · GitHub

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FROM gcc:5.3
MAINTAINER bmajoros@duke.edu

# Installs ACE from sources into /opt/
ENV DEST_DIR=/opt/

# Install GSL
ENV GSL_VERSION=2.2.1
ENV GSL=http://mirror.thecodefactory.org/gnu/gsl/gsl-${GSL_VERSION}.tar.gz
RUN curl -SLo ${DEST_DIR}/gsl-${GSL_VERSION}.tar.gz ${GSL} && \
    tar -xf ${DEST_DIR}/gsl-${GSL_VERSION}.tar.gz -C ${DEST_DIR} && \
    rm ${DEST_DIR}/gsl-${GSL_VERSION}.tar.gz && \
    cd ${DEST_DIR}/gsl-${GSL_VERSION} && \
    ./configure && \
    make && \
    make install && \
    rm -rf ${DEST_DIR}/gsl-${GSL_VERSION}

# Install R
RUN wget https://cloud.r-project.org/src/base/R-3/R-3.4.3.tar.gz && \
	tar xvfz R-3.4.3.tar.gz && \
	cd R-3.4.3 && \
	./configure && \
	make

# Install R package "glmnet"
RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
RUN /R-3.4.3/bin/Rscript -e "install.packages('glmnet')"

# Install python version 3.6
RUN wget https://www.python.org/ftp/python/3.6.3/Python-3.6.3.tgz && \
	tar xvfz Python-3.6.3.tgz && \
	cd Python-3.6.3 && \
	./configure && \
	make

# Put env in /bin so our scripts can call it normally
RUN cp /usr/bin/env /bin

# Download and install kentUtils
RUN git clone git://github.com/ENCODE-DCC/kentUtils.git && \
    cd kentUtils && \
    make && \
    cp -r ./bin/* /opt/ && \
    cd .. && \
    rm -rf kentUtils

# Download tabix from Samtools
#ENV TABIX_VERSION=0.2.6
#ENV TABIX_URL=https://sourceforge.net/projects/samtools/files/tabix/tabix-${TABIX_VERSION}.tar.bz2/download
#RUN curl -SLo ${DEST_DIR}/tabix-${TABIX_VERSION}.tar.bz2 ${TABIX_URL} && \
#    tar -xf ${DEST_DIR}/tabix-${TABIX_VERSION}.tar.bz2 -C ${DEST_DIR} && \
#    rm ${DEST_DIR}/tabix-${TABIX_VERSION}.tar.bz2 && \
#    cd ${DEST_DIR}/tabix-${TABIX_VERSION} && \
#    make && \
#    cp -r tabix ${DEST_DIR} && \
#    rm -rf ${DEST_DIR}/tabix-${TABIX_VERSION}

# Download bgzip from htslib
RUN git clone https://github.com/samtools/htslib.git && \
    cd htslib && \
    make && \
    make install

RUN git clone --recursive https://github.com/bmajoros/ACE.git && \
    export TMPDIR=/tmp && \
    export ACE=/ACE && \
    export ACEPLUS=/ACE && \
    export PERLLIB=/ACE/perl && \
    export PYTHONPATH=/ACE/python && \
    cd ACE && \
    make all

RUN cp /ACE/pam10 /root

# Setup the environment
ENV ACE=/ACE
ENV ACEPLUS=/ACE
ENV PERLLIB=/ACE/perl
ENV PYTHONPATH=/ACE/python
ENV PATH=${DEST_DIR}:/R-3.4.3/bin:/Python-3.6.3:${ACEPLUS}:${ACEPLUS}/perl:${ACEPLUS}/python:${PATH}
ENV TMPDIR=/tmp/
ENV LD_LIBRARY_PATH=/usr/local/lib