Update to latest version of Augustus (3.3)

Author: robsyme

Dockerfiles/augustus/Dockerfile

@@ -1,18 +1,30 @@
-FROM ubuntu:14.04
+FROM ubuntu:16.04
 
 MAINTAINER Rob Syme <[email protected]>
 
-RUN apt-get update && apt-get install -qqy build-essential
+RUN apt-get update \
+&& apt-get install -qqy \
+build-essential \
+libbamtools-dev \
+libboost-graph-dev \
+libboost-iostreams-dev \
+libgsl-dev \
+liblpsolve55-dev \
+libsqlite3-dev \
+libsuitesparse-dev \
+wget \
+zlib1g-dev
 
-ADD http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.1.tar.gz /opt/
-RUN cd /opt && \
-    tar -xzvf augustus* && \
-    rm -rf *.tar.gz && \
-    mv augustus* augustus && \
-    cd augustus && \
-    make
+WORKDIR /usr/local
 
-ADD fgram_base /opt/augustus/config/species/    
-ENV AUGUSTUS_CONFIG_PATH /opt/augustus/config
-ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/augustus/bin:/opt/augustus/scripts
-CMD ["/opt/augustus/bin/augustus"]
+# Install Augustus
+RUN wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus.current.tar.gz \
+&& tar -xvf augustus*.tar.gz \
+&& rm augustus*.tar.gz \
+&& cd augustus \
+&& echo "COMPGENEPRED = true" >> common.mk \
+&& make \
+&& make install
+
+ENV AUGUSTUS_CONFIG_PATH /usr/local/augustus/config
+ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/augustus/bin:/usr/local/augustus/scripts