BWA: add singularity def

src/singularity_modules/BWA/0.7.17/BWA.def

+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+BWA_VERSION=0.7.17
+SAMBLASTER_VERSION=0.1.24
+
+PACKAGES=curl="7.58.0* \
+ca-certificates=20180409 \
+build-essential=12.4* \
+zlib1g-dev=1:1.2.11*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+mv sambamba /usr/bin/ && \
+rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
+
+curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
+tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
+cd bwa-${BWA_VERSION}/ && \
+make && \
+cp bwa /usr/bin && \
+cd .. && \
+rm -R bwa-${BWA_VERSION}/
+
+curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+cd samblaster-v.${SAMBLASTER_VERSION}/ && \
+make && \
+cp samblaster /usr/bin && \
+cd .. && \
+rm -R samblaster-v.${SAMBLASTER_VERSION}/
+
+%environment
+export BWA_VERSION=0.7.17
+export SAMBLASTER_VERSION=0.1.24
+
+%runscript
+exec /bin/bash "$@"