feat(bwa-mem2): update to version 2.1

containers/bwa-mem2/Dockerfile

@@ -1,19 +1,31 @@
 ################## BASE IMAGE ######################
 
-FROM clinicalgenomics/mip:2.0
+FROM ubuntu:bionic
 
 ################## METADATA ######################
 
-LABEL base_image="clinicalgenomics/mip:2.0"
-LABEL version="1"
+LABEL base_image="ubuntu:bionic"
+LABEL version="2"
 LABEL software="bwa-mem2"
-LABEL software.version="2.0"
+LABEL software.version="2.1"
 LABEL extra.binaries="bwa-mem2"
 LABEL maintainer="Clinical-Genomics/MIP"
 
-RUN conda install bwa-mem2=2.0=he513fc3_0
+## Install curl
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    ca-certificates \
+    curl \
+    libbz2-dev \
+    libreadline-dev && \
+    apt-get clean && \
+    apt-get purge && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-## Clean up after conda
-RUN /opt/conda/bin/conda clean -tipsy
+WORKDIR /app
 
-WORKDIR /data/
+## Install bwa-mem2
+RUN curl -L https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.1/bwa-mem2-2.1_x64-linux.tar.bz2 \
+  | tar jxf -
+
+ENV PATH=/app/bwa-mem2-2.1_x64-linux:${PATH}

templates/mip_install_config.yaml

@@ -33,7 +33,7 @@ container:
   bwa-mem2:
     executable:
       bwa-mem2:
-    uri: docker.io/clinicalgenomics/bwa-mem2:2.0
+    uri: docker.io/clinicalgenomics/bwa-mem2:2.1
   bedtools:
     executable:
       bedtools: