GATK version 4.5.0.0 for gCNV (#144)

images.toml

@@ -13,6 +13,7 @@ fastqe = '0.3.1'
 fastqc = '0.11.9'
 fraser = '1.12.1'
 gatk = '4.2.6.1'
+gatk_gcnv = '4.5.0.0'
 gatk-sv_issue_661 = 'n_a'
 hap-py = '0.3.15'
 haplocheckcli = '64293b3481d52025a01a293f6cc891546c30660e'

images/gatk_gcnv/Dockerfile

@@ -0,0 +1,17 @@
+FROM debian:buster-slim
+
+ENV MAMBA_ROOT_PREFIX /root/micromamba
+ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH
+ARG VERSION=${VERSION:-4.5.0.0}
+
+RUN apt-get update && apt-get install -y git wget bash bzip2 zip && \
+    rm -r /var/lib/apt/lists/* && \
+    rm -r /var/cache/apt/* && \
+    wget -qO- https://api.anaconda.org/download/conda-forge/micromamba/0.8.2/linux-64/micromamba-0.8.2-he9b6cbd_0.tar.bz2 | tar -xvj -C /usr/local bin/micromamba && \
+    mkdir ${MAMBA_ROOT_PREFIX} && \
+    micromamba install -y --prefix ${MAMBA_ROOT_PREFIX} -c bioconda -c conda-forge \
+    gatk4=${VERSION} \
+    bcftools \
+    google-cloud-sdk \
+    && \
+    rm -r /root/micromamba/pkgs