Dockerfile to install MEDUSA (A Genome Assembler)

build-script.sh

!#/bin/bash

#apt-get update && apt-get dist-upgrade -y && apt-get install -y --no-install-recommends libnss-sss && apt-get clean all

# install python, bio-python, networkx, numpy and git (needed for Medusa)
apt-get update -qq
apt-get -y install git
apt-get -y install python python-biopython python-networkx python-numpy

# To install JAVA 8
apt-get install -y software-properties-common python-software-properties
add-apt-repository -y ppa:webupd8team/java
apt-get update
echo debconf shared/accepted-oracle-license-v1-1 select true | debconf-set-selections
echo debconf shared/accepted-oracle-license-v1-1 seen true | debconf-set-selections
apt-get install -y oracle-java8-installer

# to install ant
apt-get install -y ant

# download, install, and compile Medusa
cd /build
git clone https://github.com/combogenomics/medusa.git
cd medusa
ant
mkdir -p /usr/local/share/jars
cp -v medusa.jar /usr/local/share/jars
cp -v medusa_scripts/length_filterer.py /usr/local/bin
cp -v medusa_scripts/mmrBatch.sh /usr/local/bin
cp -v medusa_scripts/mummerRunner.sh /usr/local/bin
cp -v medusa_scripts/mummer_parser.py /usr/local/bin
cp -v medusa_scripts/netcon_mummer.py /usr/local/bin

# needed by MUMmer
apt-get -y install csh

# download and install Mummer
cd /build
wget https://downloads.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz
tar -xvzf MUMmer3.23.tar.gz
cd MUMmer3.23
make CPPFLAGS="-O3 -DSIXTYFOURBITS"
make install

cp src/kurtz/libbasedir/libbase.a /usr/local/lib
cp src/kurtz/streesrc/libstree.a /usr/local/lib

MUMMER_PROGRAMS=(
    annotate
    combineMUMs
    delta-filter
    dnadiff
    extact-tandems
    gaps
    mapview
    mgaps
    mummer
    mummerplot
    nucmer
    nucmer2xfig
    promer
    repeat-match
    run-mummer1
    run-mummer3
    show-aligns
    show-coords
    show-diff
    show-snps
    show-tiling
)

# correct library locations
for f in ${MUMMER_PROGRAMS[@]}; do
   # "fix" the perl and csh scripts;  assume C executables "work" for now
   if echo $(file ${f}) | grep 'C shell script'; then
        echo "==== Fixing: ${f} (csh) ===="
        perl -p -i.old -e 's{set bindir = /build/MUMmer3.23}{set bindir = /usr/local/bin}' ${f}
   elif echo $(file ${f}) | grep 'perl'; then
        echo "==== Fixing: ${f} (perl) ===="
        perl -p -i.old -e 's{use lib "/build/MUMmer3.23/scripts"}{use lib "/usr/local/bin/scripts"}' ${f}
        perl -p -i.old -e 's{BIN_DIR = "/build/MUMmer3.23"}{BIN_DIR = "/usr/local/bin"}' ${f}
        perl -p -i.old -e 's{AUX_BIN_DIR = "/build/MUMmer3.23/aux_bin"}{AUX_BIN_DIR = "/usr/local/bin/aux_bin"}' ${f}
        perl -p -i.old -e 's{SCRIPT_DIR = "/build/MUMmer3.23/scripts"}{SCRIPT_DIR = "/usr/local/bin/scripts"}' ${f}
   elif echo $(file ${f}) | grep ELF; then
        echo "==== Fixing ${f} (ELF) ===="
   fi
done

for f in ${MUMMER_PROGRAMS[@]}; do
    cp -v $f /usr/local/bin
done


cp -rv aux_bin /usr/local/bin/aux_bin
cp -rv scripts /usr/local/bin/scripts

# to run medusa try:
# java -jar /usr/local/share/jars/medusa.jar -scriptPath /usr/local/bin -f test/reference_genomes/ -i test/Rhodobacter_target.fna -v

Dockerfile

FROM ubuntu:16.04
MAINTAINER Pat Minx <[email protected]>

# Volumes
VOLUME /build
VOLUME /release

# bootstrap build dependencies
RUN apt-get update -qq && \
    apt-get -y install apt-transport-https && \
    apt-get update -qq && \
    apt-get -y install \
    build-essential \
    libcurl4-openssl-dev \
    ca-certificates \
    libnss-sss \
    rsync \
    curl \
    wget \
    --no-install-recommends

WORKDIR /build

# Import resources
#COPY ./L_RNA_scaffolder.tar.gz /build  # custom software you may have downloaded onto your laptop
COPY ./build-script.sh /build

RUN ["/bin/bash", "build-script.sh"]