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Former-commit-id: 1eecb206a17c4aff21d1170b48db134ce3c4f14e

organnot/Dockerfile

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+FROM ubuntu:lunar as builder
+LABEL dockerfile.version="1"
+LABEL software="phyloskims"
+
+##
+#
+# Install org-annot
+#
+##
+
+WORKDIR /
+RUN apt update  --fix-missing && apt upgrade -y
+RUN apt install -y build-essential 
+RUN apt install -y git tcsh bash gawk parallel gettext zlib1g-dev libglib2.0-0
+RUN git clone https://git.metabarcoding.org/org-asm/org-annotate.git
+
+#
+# Compile tools
+#
+
+WORKDIR /org-annotate/src
+RUN make
+
+
+##
+#
+# Install Organelle Assembler
+#
+##
+
+WORKDIR "/" 
+RUN apt install -y python3-pip python3-dev python3-venv
+RUN git clone https://git.metabarcoding.org/org-asm/org-asm.git
+RUN python3 -m venv org-assembler 
+WORKDIR "/org-asm" 
+RUN bash -c '../org-assembler/bin/pip3 install -r requirements.txt'
+RUN bash -c '../org-assembler/bin/python3 setup.py install --no-serenity' 
+WORKDIR "/" 
+
+##
+#
+# Install the final image grouping previously compiled softwares
+#
+##
+
+FROM ubuntu:lunar as phyloskims
+WORKDIR /
+RUN apt update  --fix-missing && apt upgrade -y
+RUN apt install -y tcsh bash gawk parallel zlib1g libglib2.0-0 clustalo muscle cd-hit hmmer
+COPY --from=builder /org-annotate /org-annotate
+RUN rm -rf /org-annotate/src
+COPY --from=builder /org-assembler /org-assembler
+COPY --from=builder /org-assembler/bin/oa /bin
+COPY organnot /bin
+RUN  chmod +x /bin/organnot
+#
+# Recompile HMMER models
+#
+WORKDIR /org-annotate/data/its/ITSx_db/HMMs
+RUN rm *.h3*
+RUN for f in *.hmm ; do hmmpress $f ; done
+WORKDIR /
+
+RUN mkdir -p /data
+WORKDIR /data

organnot/organnot

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+#!/bin/bash
+
+/org-annotate/org-annotate.sh $*