added samtools to whatshap

docker-whatshap/Dockerfile

@@ -1,8 +1,42 @@
 FROM ghcr.io/dhslab/docker-python3:latest
 
-LABEL Image with whatshap
+LABEL Image with htslib, samtools and whatshap
 
 # update as needed
 RUN apt-get update -y && apt-get install -y --no-install-recommends
 
+##############
+#HTSlib 1.18#
+##############
+ENV HTSLIB_INSTALL_DIR=/opt/htslib
+
+WORKDIR /tmp
+RUN wget --no-check-certificate https://github.com/samtools/htslib/releases/download/1.18/htslib-1.18.tar.bz2 && \
+    tar --bzip2 -xvf htslib-1.18.tar.bz2 && \
+    cd /tmp/htslib-1.18 && \
+    ./configure  --enable-plugins --prefix=$HTSLIB_INSTALL_DIR && \
+    make && \
+    make install && \
+    cp $HTSLIB_INSTALL_DIR/lib/libhts.so* /usr/lib/ && \
+    ln -s $HTSLIB_INSTALL_DIR/bin/tabix /usr/bin/tabix && \
+    ln -s $HTSLIB_INSTALL_DIR/bin/bgzip /usr/bin/bgzip && \
+    rm -Rf /tmp/htslib-1.18
+
+################
+#Samtools 1.18#
+################
+ENV SAMTOOLS_INSTALL_DIR=/opt/samtools
+
+WORKDIR /tmp
+RUN wget --no-check-certificate https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2 && \
+    tar --bzip2 -xf samtools-1.18.tar.bz2 && \
+    cd /tmp/samtools-1.18 && \
+    ./configure --with-htslib=$HTSLIB_INSTALL_DIR --prefix=$SAMTOOLS_INSTALL_DIR && \
+    make && \
+    make install && \
+    ln -s /opt/samtools/bin/* /usr/local/bin/ && \
+    cd / && \
+    rm -rf /tmp/samtools-1.18
+
+
 RUN pip3 install whatshap