Fraser (#130)

* outrider dockerfile * update docker file for outrider * fraser image * update images.toml with fraser version
populationgenomics · Feb 5, 2024 · 1fb1da2 · 1fb1da2
1 parent f02ac22
commit 1fb1da2
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diff --git a/images.toml b/images.toml
@@ -9,6 +9,7 @@ expansionhunter_bw2 = 'b85cba004fba4e0223e632fae576bc7fad0da804'
 fastp = '0.23.4'
 fastqe = '0.3.1'
 fastqc = '0.11.9'
+fraser = '1.12.1'
 gatk = '4.2.6.1'
 hap-py = '0.3.15'
 haplocheckcli = '64293b3481d52025a01a293f6cc891546c30660e'

diff --git a/images/fraser/Dockerfile b/images/fraser/Dockerfile
@@ -0,0 +1,15 @@
+FROM debian:bookworm-slim
+
+ENV MAMBA_ROOT_PREFIX /root/micromamba
+ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH
+ARG VERSION=${VERSION:-1.12.1}
+
+RUN apt-get update && apt-get install -y git wget bash bzip2 zip && \
+    rm -r /var/lib/apt/lists/* && \
+    rm -r /var/cache/apt/* && \
+    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 ${MAMBA_ROOT_PREFIX} -c bioconda -c conda-forge \
+    python=3.10 r-base=4.3.1 r-reshape2=1.4.4 r-tidyverse=2.0.0 \
+    bioconductor-fraser=${VERSION} bioconductor-txdb.hsapiens.ucsc.hg38.knowngene bioconductor-org.hs.eg.db && \
+    rm -r /root/micromamba/pkgs