Update Dockerfile to use samtools zlibng image

- Add bwa-mem2
- #325

src/bwamaptools/Dockerfile

@@ -1,38 +1,6 @@
-FROM debian:buster-slim
+FROM vibsinglecellnf/samtools:1.12
 
 ENV DEBIAN_FRONTEND=noninteractive
-RUN BUILDPKGS="build-essential \
-        autoconf cmake git \
-        automake make gcc perl bedtools \
-        libbz2-dev \
-        libcurl4-openssl-dev \
-        libssl-dev \
-        zlib1g-dev \
-        liblzma-dev \
-        curl \
-        libncurses5-dev"&& \
-    apt-get update && \
-    apt-get install -y --no-install-recommends apt-utils debconf locales && dpkg-reconfigure locales && \
-    apt-get install -y --reinstall ca-certificates && \
-    apt-get install -y --no-install-recommends $BUILDPKGS
-
-# Install htslib
-RUN git clone --recurse-submodules https://github.com/samtools/htslib.git && \
-    cd htslib && \
-    autoheader && \
-    autoconf && \
-    ./configure --prefix=/usr/local/ && \
-    make && \
-    make install
-
-# Install SAMtools
-RUN git clone https://github.com/samtools/samtools.git && \
-    cd samtools && \
-    autoheader && \
-    autoconf -Wno-syntax && \
-    ./configure --prefix=/usr/local/ && \
-    make && \
-    make install
 
 # install bwa
 RUN git clone https://github.com/lh3/bwa.git && \
@@ -41,16 +9,12 @@ RUN git clone https://github.com/lh3/bwa.git && \
     mv /bwa/bwa /usr/local/bin/
 
 # install bwa-mem2
-ENV BWAMEM2_VER 2.1
+ENV BWAMEM2_VER 2.2.1
 RUN cd /tmp && \
     curl -L https://github.com/bwa-mem2/bwa-mem2/releases/download/v${BWAMEM2_VER}/bwa-mem2-${BWAMEM2_VER}_x64-linux.tar.bz2 | tar jxf - && \
     mv bwa-mem2-${BWAMEM2_VER}_x64-linux/bwa-mem2* /usr/local/bin
 
-RUN apt-get -y update && \
-    apt-get -y --no-install-recommends install \
-        # Need to run ps
-        procps \
-        less && \
-    rm -rf /var/cache/apt/* && \
-    rm -rf /var/lib/apt/lists/*
+RUN rm -rf /var/cache/apt/* && \
+    rm -rf /var/lib/apt/lists/* && \
+    ldconfig