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Dockerfile
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FROM ubuntu:xenial
MAINTAINER David Spencer <[email protected]>
LABEL \
description="Haley's Walkers"
RUN apt-get update -y && apt-get install -y \
ant \
apt-utils \
build-essential \
bzip2 \
default-jdk \
default-jre \
gcc-multilib \
git \
libncurses5-dev \
libnss-sss \
nodejs \
tzdata \
unzip \
wget \
zlib1g-dev \
perl \
expat \
libexpat-dev
##########
#Haley's GATK 3.6#
##########
#ENV maven_package_name apache-maven-3.3.9
#RUN cd /tmp/ && wget -q http://mirror.nohup.it/apache/maven/maven-3/3.3.9/binaries/apache-maven-3.3.9-bin.zip
WORKDIR /opt
RUN git clone -b dev --recursive https://github.com/abelhj/gatk.git
#RUN cd /opt/ && unzip /tmp/${maven_package_name}-bin.zip \
# && rm -rf /tmp/${maven_package_name}-bin.zip LICENSE NOTICE README.txt \
# && cd /opt/ \
# && cd /opt/gatk && /opt/${maven_package_name}/bin/mvn verify -P\!queue
ENV SAMTOOLS_INSTALL_DIR=/opt/samtools
WORKDIR /tmp
RUN wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 && \
tar --bzip2 -xf samtools-1.3.1.tar.bz2
WORKDIR /tmp/samtools-1.3.1
RUN ./configure --enable-plugins --prefix=$SAMTOOLS_INSTALL_DIR && \
make all all-htslib && \
make install install-htslib
WORKDIR /
RUN ln -s $SAMTOOLS_INSTALL_DIR/bin/samtools /usr/bin/samtools && \
rm -rf /tmp/samtools-1.3.1
WORKDIR /opt
ADD CalculateContamination.pl /opt/