Merge pull request #9 from EichlerLab/main

Author: kvg

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
+