Add Dockerfiles with zlib-ng

- vibsinglecellnf/samtools:base-0.1 has zlib-ng and libdeflate on a
debian base image
- vibsinglecellnf/samtools:1.12 uses the base-0.1 image, and includes
htslib and samtools
- #325

src/samtools/Dockerfile

@@ -0,0 +1,47 @@
+FROM vibsinglecellnf/samtools:base-0.1
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN BUILDPKGS="git \
+        autoconf \
+        automake \
+        perl \
+        zlib1g-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libcurl4-openssl-dev \
+        libssl-dev \
+        bedtools \
+        libncurses5-dev" && \
+    apt-get update && \
+    apt-get install -y --no-install-recommends $BUILDPKGS
+
+# install htslib
+# Include fix so HTSlib works with zlib-ng: https://github.com/samtools/htslib/compare/develop...jkbonfield:zlib-ng-fix
+ENV HTSLIB_VERSION 1.12
+RUN curl -L -o /tmp/htslib-${HTSLIB_VERSION}.tar.bz2 \
+        https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2 && \
+    mkdir -p /tmp/htslib-${HTSLIB_VERSION} && \
+    tar jxvf /tmp/htslib-${HTSLIB_VERSION}.tar.bz2 -C /tmp/htslib-${HTSLIB_VERSION} --strip-components 1 && \
+    cd /tmp/htslib-${HTSLIB_VERSION} && \
+    curl -L -O https://raw.githubusercontent.com/jkbonfield/htslib/715056cdd3f85855a503ac932f58e84b92c7dd0e/bgzf.c && \
+    ./configure \
+        CFLAGS="-fPIC" && \
+    make && \
+    make install && \
+    cd .. && rm -rf htslib-${HTSLIB_VERSION}*
+
+# install samtools
+ENV SAMTOOLS_VERSION 1.12
+RUN curl -L -o /tmp/samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+        https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
+    mkdir -p /tmp/samtools-${SAMTOOLS_VERSION} && \
+    tar jxvf /tmp/samtools-${SAMTOOLS_VERSION}.tar.bz2 -C /tmp/samtools-${SAMTOOLS_VERSION} --strip-components 1 && \
+    cd /tmp/samtools-${SAMTOOLS_VERSION} && \
+    ./configure && \
+    make && \
+    make install && \
+    cd .. && rm -rf samtools-${SAMTOOLS_VERSION}*
+
+RUN rm -rf /var/cache/apt/* && \
+    rm -rf /var/lib/apt/lists/*
+

src/samtools/Dockerfile.samtools-base

@@ -0,0 +1,37 @@
+FROM debian:buster-slim
+
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        apt-utils debconf locales locales-all && \
+    dpkg-reconfigure locales && \
+    apt-get install -y --reinstall ca-certificates && \
+    apt-get install -y --no-install-recommends \
+        cmake \
+        make \
+        gcc \
+        libbz2-dev \
+        zlib1g-dev \
+        liblzma-dev \
+        libdeflate-dev \
+        bzip2 \
+        pigz \
+        curl \
+        procps \
+        less
+
+# zlib-ng
+ENV ZLIBNG 2.0.2
+RUN curl -L -o /tmp/zlib-ng-${ZLIBNG}.tar.gz https://github.com/zlib-ng/zlib-ng/archive/refs/tags/${ZLIBNG}.tar.gz && \
+    cd /tmp && tar xvf zlib-ng-${ZLIBNG}.tar.gz && \
+    cd zlib-ng-${ZLIBNG} && \
+    cmake -DZLIB_COMPAT=ON -DINSTALL_UTILS=ON . && \
+    cmake --build . --config Release && \
+    ctest --verbose -C Release && \
+    cmake --build . --target install && \
+    cd .. && rm -r zlib-ng-${ZLIBNG}*
+
+RUN rm -rf /var/cache/apt/* && \
+    rm -rf /var/lib/apt/lists/* && \
+    ldconfig
+