Sambamba (#113)

* sambamba * add sambamba version to images.toml --------- Co-authored-by: Michael Franklin <[email protected]>
populationgenomics · Oct 24, 2023 · f00092b · f00092b
1 parent 6bb138d
commit f00092b
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diff --git a/images.toml b/images.toml
@@ -19,6 +19,7 @@ picard = '2.27.4'
 reviewer = '0.2.7'
 reviewer_bw2 = '0.2.7-bw2-fork-0.2'
 saige-qtl = '1bdfe8408a17f7da8b0453a697a867f412f48bcc'
+sambamba = '1.0.1'
 samblaster = '0.1.26'
 samtools = '1.16.1'
 scanpy = '1.9.3'

diff --git a/images/sambamba/Dockerfile b/images/sambamba/Dockerfile
@@ -0,0 +1,13 @@
+FROM debian:bookworm-slim
+
+ARG VERSION=${VERSION:-1.0.1}
+
+RUN apt-get update && apt-get install -y git wget bash bzip2 zip && \
+    rm -r /var/lib/apt/lists/* && \
+    rm -r /var/cache/apt/* && \
+    mkdir -p /tmp/sambamba && \
+    cd /tmp/sambamba && \
+    wget https://github.com/biod/sambamba/releases/download/v${VERSION}/sambamba-${VERSION}-linux-amd64-static.gz && \
+    gunzip sambamba-${VERSION}-linux-amd64-static.gz && \
+    mv sambamba-${VERSION}-linux-amd64-static /usr/local/bin/sambamba && \
+    chmod a+x /usr/local/bin/sambamba