Subread (#114)

* add subread image * add subread version to images.toml --------- Co-authored-by: Michael Franklin <[email protected]>
populationgenomics · Oct 24, 2023 · a0e94e8 · a0e94e8
1 parent f00092b
commit a0e94e8
Show file tree

Hide file tree

Showing 2 changed files with 15 additions and 0 deletions.
diff --git a/images.toml b/images.toml
@@ -25,6 +25,7 @@ samtools = '1.16.1'
 scanpy = '1.9.3'
 somalier = '0.2.15'
 star = '2.7.10b'
+subread = '2.0.6'
 trtools = '5.0.2'
 vep_105 = '105.0'
 vep_110 = 'release_110.1'

diff --git a/images/subread/Dockerfile b/images/subread/Dockerfile
@@ -0,0 +1,14 @@
+FROM debian:bookworm-slim
+
+ENV MAMBA_ROOT_PREFIX /root/micromamba
+ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH
+ARG VERSION=${VERSION:-2.0.6}
+
+RUN apt-get update && apt-get install -y git wget bash bzip2 zip curl && \
+    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 ${MAMBA_ROOT_PREFIX} -c bioconda -c conda-forge \
+    subread=${VERSION} && \
+    rm -r /root/micromamba/pkgs