hisat2: add samtools to singularity modules

src/singularity_modules/hisat2/2.0.0/hisat2.def

 Bootstrap: docker
-From: ubuntu:18.04
+From: alpine:3.8
 
 %labels
-MAINTAINER Nicolas Fontrodona
+MAINTAINER Laurent Modolo
 
 %post
+SAMTOOLS_VERSION=1.7
 HISAT2_VERSION=2.0.0
-PACKAGES="unzip \
-gcc \
-g++ \
-make \
-curl \
-ca-certificates"
+PACKAGES="git \
+          make \
+          gcc \
+          musl-dev \
+          zlib-dev \
+          ncurses-dev \
+          bzip2-dev \
+          xz-dev \
+          bash \
+          curl \
+          zip \
+          g++ \
+          perl \
+          python"
+apk update && \
+apk add ${PACKAGES}
 
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
+git clone https://github.com/samtools/htslib.git && \
+cd htslib && \
+git checkout ${SAMTOOLS_VERSION}  && \
+cd .. && \
+git clone https://github.com/samtools/samtools.git && \
+cd samtools && \
+git checkout ${SAMTOOLS_VERSION} && \
+make && \
+cp samtools /usr/bin/
 
 curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
 unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
@@ -26,6 +43,7 @@ cp hisat2-* /usr/bin && \
 rm -Rf hisat2-${HISAT2_VERSION}-beta
 
 %environment
+export SAMTOOLS_VERSION=1.7
 export HISAT2_VERSION=2.0.0
 
 %runscript