Add LPerlaza/fromAssembly2Feature container

.github/workflows/docker-build-push.yml

@@ -29,6 +29,10 @@ jobs:
           - path: ./dockerfiles/superfreq
             image: ghcr.io/monashbioinformaticsplatform/containers/superfreq
             version: 1.4.5
+            enabled: false
+          - path: ./dockerfiles/fromassembly2feature
+            image: ghcr.io/monashbioinformaticsplatform/containers/fromassembly2feature
+            version: 2.22-a1805f6
             enabled: true
 
     steps:

dockerfiles/fromassembly2feature/2.22-a1805f6/Dockerfile

@@ -0,0 +1,32 @@
+FROM mambaorg/micromamba:1.5.6
+
+ENV GIT_REF=a1805f682c9ac28c3ec22dc067d3576e64764fb3
+
+# TODO: Pin versions
+RUN micromamba install -y -n base \
+    bioconda::prodigal \
+    bioconda::samtools \
+    bioconda::blast \
+    bioconda::plasclass \
+    r::r-essentials \
+    bioconda::bioconductor-msa \
+    bioconda::bioconductor-biostrings \
+    conda-forge::r-seqinr \
+    conda-forge::r-reshape2 \
+    conda-forge::r-rmarkdown \
+    conda-forge::pandoc && \
+    micromamba clean --all --yes
+
+USER root
+
+RUN apt-get update && apt-get install -y git && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+RUN git clone https://github.com/LPerlaza/fromAssembly2Feature.git /opt/fromAssembly2Feature && \
+    cd /opt/fromAssembly2Feature && \
+    git checkout ${GIT_REF} && \
+    chmod +x /opt/fromAssembly2Feature/fromAssembly2gene.pl && \
+    ln -s /opt/fromAssembly2Feature/fromAssembly2gene.pl /usr/bin/fromAssembly2gene.pl
+
+USER $MAMBA_USER
+
+CMD ["fromAssembly2gene.pl"]