update Patchwork from v0.5.2 to v0.5.5

patchwork/0.5.5/Dockerfile

@@ -0,0 +1,86 @@
+# To reduce the final image size, the build process has been split into a build
+# stage and a production stage. After compiling Patchwork, the Julia
+# installation is no longer needed and is therefore removed in the second stage.
+
+# Stage 1/2: Build
+# ----------------
+
+# Set the base image
+FROM ubuntu:22.04 AS builder
+
+# System is non-interactive when building the Docker image
+ENV DEBIAN_FRONTEND noninteractive
+
+# Set time zone to Zurich, Europe
+ENV TZ=Europe/Zurich
+RUN ln -snf "/usr/share/zoneinfo/${TZ}" /etc/localtime && echo "$TZ" > /etc/timezone
+
+# Update the repository sources and install required tools and libraries
+RUN apt-get update && apt-get install --yes --no-install-recommends \
+    apt-utils \
+    wget \
+    gcc \
+    ca-certificates \
+    python3-matplotlib \
+    libqt5widgets5 \
+    git
+
+# Set work directory
+WORKDIR '/opt'
+
+# Download and install Julia
+RUN wget --quiet 'https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.3-linux-x86_64.tar.gz' \
+    && tar -xvzf 'julia-1.9.3-linux-x86_64.tar.gz' \
+    && rm 'julia-1.9.3-linux-x86_64.tar.gz'
+ENV PATH "/opt/julia-1.9.3/bin:${PATH}"
+
+# Download and install DIAMOND
+RUN wget 'http://github.com/bbuchfink/diamond/releases/download/v2.1.8/diamond-linux64.tar.gz' \
+    && tar -xvzf 'diamond-linux64.tar.gz' \
+    && mv 'diamond' '/usr/local/bin' \
+    && rm 'diamond-linux64.tar.gz'
+
+# Download and install Patchwork
+RUN git clone 'https://github.com/fethalen/patchwork' \
+    && cd patchwork/build \
+    && ./build_app.jl
+
+# Stage 2/2: Production
+# ---------------------
+
+# Set the base image
+FROM ubuntu:22.04 AS production
+
+# Metadata
+LABEL org.opencontainers.image.authors="[email protected]"
+LABEL version="1"
+LABEL software="Patchwork"
+LABEL software.version="0.5.5"
+LABEL about.author="Felix Thalén <[email protected]>"
+LABEL about.summary="Alignment-based Exon Retrieval and Concatenation with Phylogenomic Applications"
+LABEL about.home="https://github.com/fethalen/patchwork"
+LABEL about.documentation="https://github.com/fethalen/patchwork#readme"
+LABEL about.license="SPDX:GPL-3.0"
+LABEL about.tags="phylogenomics, phylogenetics, genomics, alignment"
+
+# System is non-interactive when building the Docker image
+ENV DEBIAN_FRONTEND noninteractive
+
+# Set time zone to Zurich, Europe
+ENV TZ=Europe/Zurich
+RUN ln -snf "/usr/share/zoneinfo/${TZ}" /etc/localtime && echo "$TZ" > /etc/timezone
+
+# Create the user
+RUN useradd --create-home --shell /bin/bash --user-group --uid 1000 patchwork
+
+# Set the default user
+USER patchwork
+
+# Set the working directory
+WORKDIR /home/patchwork
+
+COPY --from=builder /opt/patchwork/build/compiled /opt/patchwork
+COPY --from=builder /usr/local/bin/diamond /usr/local/bin/diamond
+ENV PATH /opt/patchwork/bin:$PATH
+
+ENTRYPOINT ["patchwork"]