# Base Image FROM ubuntu:18.04 # Metadata LABEL base.image="ubuntu:18.04" LABEL software="TPMCalculator" LABEL software.version="0.0.3" LABEL description="This program calculates the TPM (Transcript per Millions) values for the exons and introns from NGS RNA-Seq aligned reads (BAM files)" LABEL website="https://github.com/ncbi/TPMCalculator" LABEL documentation="https://github.com/ncbi/TPMCalculator" LABEL license="http://www.gnu.org/licenses/" LABEL tags="RNA-seq" # Maintainer MAINTAINER Roberto Vera Alvarez ENV URL=https://github.com/ncbi/TPMCalculator ENV BAMTOOLS_URL=https://github.com/pezmaster31/bamtools ENV FOLDER=TPMCalculator ENV BAMTOOLS_FOLDER=bamtools ENV DST=/tmp ENV BAMTOOLS_DIR=/usr/local ENV CPPFLAGS="-I $BAMTOOLS_DIR/include/bamtools" ENV LDFLAGS="-L $BAMTOOLS_DIR/lib/bamtools -Wl,-rpath,$BAMTOOLS_DIR/lib/bamtools" USER root RUN apt-get clean all && \ apt-get update && \ apt-get -y upgrade && \ apt-get install -y apt-utils && \ apt-get install -y tzdata && \ apt-get install -y software-properties-common && \ apt-get install -y gcc g++ perl wget zip make && \ apt-get install -y unzip cmake git libjsoncpp-dev zlib1g-dev && \ apt-get clean && \ apt-get purge && \ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* RUN cd $DST && \ git clone $BAMTOOLS_URL && \ cd $BAMTOOLS_FOLDER && \ mkdir build && \ cd build && \ cmake .. && \ make && \ make install && \ cd $DST && \ rm -rf $BAMTOOLS_FOLDER RUN cd $DST && \ git clone $URL && \ cd $FOLDER && \ make && \ mv $DST/$FOLDER/bin/* /usr/local/bin/ && \ rm -rf $DST/$FOLDER RUN adduser --disabled-password --gecos '' ubuntu RUN chmod a+rwx /home/ubuntu/ RUN mkdir /home/ubuntu/bin RUN chown -R ubuntu /home/ubuntu USER ubuntu WORKDIR /data/ CMD ["TPMCalculator"]