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Dockerfile
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# Set the base image to Debian
FROM debian:latest
# File Author / Maintainer
MAINTAINER Tiffany Delhomme <[email protected]>
RUN apt-get clean && \
apt-get update -y && \
# Install dependences
DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
g++ \
make \
zlib1g-dev \
libncurses5-dev \
ca-certificates \
dialog \
wget \
bzip2 && \
# Install samtools
wget https://github.com/samtools/samtools/releases/download/1.3/samtools-1.3.tar.bz2 && \
tar -jxf samtools-1.3.tar.bz2 && \
cd samtools-1.3 && \
make && \
make install && \
cd .. && \
rm -rf samtools-1.3 samtools-1.3.tar.bz2 && \
# Install bwa
wget -q http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.13.tar.bz2 \
tar xjf bwa-0.7.13.tar.bz2 \
cd bwa-0.7.13 \
sed -i 's/CFLAGS=\\t\\t-g -Wall -Wno-unused-function -O2/CFLAGS=-g -Wall -Wno-unused-function -O2 -static/' Makefile \
make \
cp -p bwa /usr/local/bin \
cd .. \
rm -rf bwa-0.7.13* && \
# Install sambamba
wget https://github.com/lomereiter/sambamba/releases/download/v0.5.9/sambamba_v0.5.9_linux.tar.bz2 \
tar jxf sambamba_v0.5.9_linux.tar.bz2 \
chmod +x sambamba_v0.5.9 \
cp -p sambamba_v0.5.9 /usr/local/bin/sambamba \
rm -rf sambamba_v0.5.9_linux.tar.bz2 \
rm sambamba_v0.5.9 && \
# Install samblaster
wget https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.22/samblaster-v.0.1.22.tar.gz \
tar zxvf samblaster-v.0.1.22.tar.gz \
cd samblaster-v.0.1.22 \
make \
cp samblaster /usr/local/bin/ \
cd .. \
rm -rf samblaster-v.0.1.22* && \
# Remove unnecessary dependences
DEBIAN_FRONTEND=noninteractive apt-get remove -y \
g++ \
make \
zlib1g-dev \
libncurses5-dev \
dialog \
wget \
bzip2 \
software-properties-common && \
# Clean
DEBIAN_FRONTEND=noninteractive apt-get autoremove -y && \
apt-get clean