Merge pull request #153 from sanger-pathogens/RT666089_docker_build_bust

docker build required 2 extra  debian packages

Dockerfile

@@ -2,11 +2,27 @@
 #
 FROM debian:testing
 
+ENV   BUILD_DIR=/opt/circlator
+
 # Install the dependancies
-RUN apt-get update -qq && apt-get install -y python python3-pip git wget unzip zlib1g-dev libncurses5-dev
+RUN   apt-get update -qq && apt-get install -y python python3-pip git wget unzip zlib1g-dev libncurses5-dev
+
+RUN   apt-get install --yes libbz2-dev liblzma-dev
+
+RUN   mkdir -p ${BUILD_DIR}
+COPY  . ${BUILD_DIR}
+
+RUN   cd ${BUILD_DIR} && ./install_dependencies.sh
+ENV   PATH ${BUILD_DIR}/build/bwa-0.7.12:${BUILD_DIR}/build/canu-1.4/Linux-amd64/bin/:${BUILD_DIR}/build/prodigal-2.6.2:${BUILD_DIR}/build/samtools-1.3:${BUILD_DIR}/build/MUMmer3.23:${BUILD_DIR}/build/SPAdes-3.7.1-Linux/bin:$PATH
+RUN   export PATH
+RUN   cd ${BUILD_DIR} && python3 setup.py install
+
+RUN   circlator progcheck
 
-RUN git clone https://github.com/sanger-pathogens/circlator.git
-RUN cd circlator && ./install_dependencies.sh
-ENV PATH /circlator/build/bwa-0.7.12:/circlator/build/canu-1.4/Linux-amd64/bin/:/circlator/build/prodigal-2.6.2:/circlator/build/samtools-1.3:/circlator/build/MUMmer3.23:/circlator/build/SPAdes-3.7.1-Linux/bin:$PATH
-RUN export PATH
-RUN cd circlator && python3 setup.py install
+CMD   echo "Usage:  docker run -v \`pwd\`:/var/data -it <IMAGE_NAME> bash" && \
+      echo "" && \
+      echo "This will place you in a shell with your current working directory accessible as /var/data." && \
+      echo "You can then run commands like:" && \
+      echo "   circlator all /var/data/assembly.fasta /var/data/reads /var/data/<output_subdirectory>" && \
+      echo "For help, please go to https://github.com/sanger-pathogens/circlator/wiki, or type" && \
+      echo "   circlator --help"