diff --git a/docker/augustus/Dockerfile b/docker/augustus/Dockerfile new file mode 100644 index 0000000..d0757b1 --- /dev/null +++ b/docker/augustus/Dockerfile @@ -0,0 +1,54 @@ +FROM ubuntu:20.04 + +# Set timezone in tzdata +ENV DEBIAN_FRONTEND="noninteractive" TZ="Europe/Berlin" + +# Install required packages +RUN apt-get update +RUN apt-get install -y build-essential wget git autoconf + +# Install dependencies for AUGUSTUS comparative gene prediction mode (CGP) +RUN apt-get install -y libgsl-dev libboost-all-dev libsuitesparse-dev liblpsolve55-dev +RUN apt-get install -y libsqlite3-dev libmysql++-dev + +# Install dependencies for the optional support of gzip compressed input files +RUN apt-get install -y libboost-iostreams-dev zlib1g-dev + +# Install dependencies for bam2hints and filterBam +RUN apt-get install -y libbamtools-dev + +# Install additional dependencies for bam2wig +RUN apt-get install -y samtools libhts-dev + +# Install additional dependencies for homGeneMapping and utrrnaseq +RUN apt-get install -y libboost-all-dev + +# Install additional dependencies for scripts +RUN apt-get install -y cdbfasta diamond-aligner libfile-which-perl libparallel-forkmanager-perl libyaml-perl libdbd-mysql-perl +RUN apt-get install -y --no-install-recommends python3-biopython + +# Install hal - required by homGeneMapping +# execute the commented out code if you want to use this program - see auxprogs/homGeneMapping/Dockerfile +#RUN apt-get install -y libhdf5-dev +#RUN git clone https://github.com/benedictpaten/sonLib.git /opt/sonLib +#WORKDIR /opt/sonLib +#RUN make +#RUN git clone https://github.com/ComparativeGenomicsToolkit/hal.git /opt/hal +#WORKDIR /opt/hal +#ENV RANLIB=ranlib +#RUN make +#ENV PATH="${PATH}:/opt/hal/bin" + +# Clone AUGUSTUS repository +ADD / /root/augustus + +# Build AUGUSTUS +WORKDIR "/root/augustus" +RUN make clean +RUN make +RUN make install +ENV PATH="/root/augustus/bin:/root/augustus/scripts:${PATH}" + +# Test AUGUSTUS +RUN make unit_test +