fixed issues with Docker and added Apptainer/Singularity support

docker/Dockerfile

@@ -11,19 +11,19 @@ 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
-
-# RUN groupadd --gid 1000 patchwork \
-#     && useradd --uid 1000 --gid patchwork --shell /bin/bash --create-home patchwork \
-#     && chmod -R a+rwx /home/patchwork
-# USER patchwork
+    libqt5widgets5 \
+    git
 
 # Set work directory
 WORKDIR '/opt'
@@ -32,67 +32,55 @@ WORKDIR '/opt'
 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-rc3/bin:${PATH}"
+ENV PATH "/opt/julia-1.9.3/bin:${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'
 
-# Doad and install Patchwork
-ARG PATCHWORK_VERSION='0.5.2'
-RUN wget -O "patchwork-${PATCHWORK_VERSION}.tar.gz" "https://github.com/fethalen/Patchwork/archive/refs/tags/v${PATCHWORK_VERSION}.tar.gz" \
-    && tar -xvzf "patchwork-${PATCHWORK_VERSION}.tar.gz" \
-    && rm "patchwork-${PATCHWORK_VERSION}.tar.gz" \
-    && cd "Patchwork-${PATCHWORK_VERSION}" \
-    && julia --project=. -e "import Pkg; Pkg.instantiate()" \
-    && julia --project=. src/compile.jl . src/precompiled.jl ../patchwork-$VERSION
-
+# Download and install Patchwork
 RUN git clone 'https://github.com/fethalen/patchwork' \
-    && cd patchwork \
-    && julia --project=. -e 'import Pkg; Pkg.instantiate()' \
-    && julia --project=. src/compile.jl . src/precompiled.jl ../patchwork-$VERSION
-
-# # Stage 2/2: Production
-# # ---------------------
-
-# # Set the base image
-# FROM ubuntu:22.04
-
-# # File maintainer
-# MAINTAINER Felix Thalén <[email protected]>
-
-# # System is non-interactive when building the Docker image
-# ENV DEBIAN_FRONTEND noninteractive
-
-# # Set time zone to Zurich, Europe
-# ENV TZ=Europe/Zurich
-# RUN ln -snf "/usr/share/zoneinfo/${TZ}" /etc/localtime && echo "$TZ" > /etc/timezone
-
-# # Metadata
-# LABEL base_image="ubuntu:20.04"
-# LABEL version="1"
-# LABEL software="Patchwork"
-# LABEL software.version="0.5.2"
-# LABEL about.author="Felix Thalén <[email protected]>"
-# LABEL about.summary="Alignment-based Exon Retrieval and Concatenation with Phylogenomic Applications"
-# LABEL about.home="https://github.com/fethalen/Patchwork"
-# LABEL about.documentation="https://github.com/fethalen/Patchwork#readme"
-# LABEL about.license="SPDX:GPL-3.0"
-# LABEL about.license_file="https://github.com/fethalen/Patchwork/blob/main/LICENSE"
-# LABEL about.tags="phylogenomics"
-
-# RUN groupadd --gid 1000 patchwork \
-#     && useradd --uid 1000 --gid patchwork --shell /bin/bash --create-home patchwork \
-#     && chmod -R a+rwx /home/patchwork
-# WORKDIR /home/patchwork
-# USER patchwork
-# ENV VERSION 0.5.2
-
-# COPY --from=builder /home/patchwork/patchwork-$VERSION patchwork-$VERSION
-# COPY --from=builder /home/patchwork/diamond diamond
-# RUN ln -s patchwork-$VERSION/bin/patchwork patchwork
-# ENV PATH /home/patchwork:$PATH
-
-# CMD patchwork --help
+    && cd patchwork/build \
+    && ./build_app.jl
+
+# Stage 2/2: Production
+# ---------------------
+
+# Set the base image
+FROM ubuntu:22.04 AS production
+
+# Metadata
+LABEL org.opencontainers.image.authors="[email protected]"
+LABEL version="1"
+LABEL software="Patchwork"
+LABEL software.version="0.5.5"
+LABEL about.author="Felix Thalén <[email protected]>"
+LABEL about.summary="Alignment-based Exon Retrieval and Concatenation with Phylogenomic Applications"
+LABEL about.home="https://github.com/fethalen/patchwork"
+LABEL about.documentation="https://github.com/fethalen/patchwork#readme"
+LABEL about.license="SPDX:GPL-3.0"
+LABEL about.tags="phylogenomics, phylogenetics, genomics, alignment"
+
+# System is non-interactive when building the Docker image
+ENV DEBIAN_FRONTEND noninteractive
+
+# Set time zone to Zurich, Europe
+ENV TZ=Europe/Zurich
+RUN ln -snf "/usr/share/zoneinfo/${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"]

docker/patchwork.def

@@ -0,0 +1,112 @@
+Bootstrap: docker
+From: ubuntu:22.04 
+Stage: builder
+
+%post
+# 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
+
+# System is non-interactive when building the Docker image
+DEBIAN_FRONTEND=noninteractive
+
+# Set time zone to Zurich, Europe
+TZ=Europe/Zurich
+ln -snf "/usr/share/zoneinfo/${TZ}" /etc/localtime && echo "$TZ" > /etc/timezone
+
+# Update the repository sources and install required tools and libraries
+apt-get update && apt-get install --yes --no-install-recommends \
+apt-utils \
+wget \
+gcc \
+ca-certificates \
+python3-matplotlib \
+libqt5widgets5 \
+git
+
+# Set work directory
+mkdir -p '/opt'
+cd '/opt'
+
+# Download and install Julia
+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'
+PATH="/opt/julia-1.9.3/bin:${PATH}"
+
+# Download and install DIAMOND
+wget 'http://github.com/bbuchfink/diamond/releases/download/v2.1.8/diamond-linux64.tar.gz' \
+&& tar -xvzf 'diamond-linux64.tar.gz' \
+&& mv 'diamond' '/usr/local/bin' \
+&& rm 'diamond-linux64.tar.gz'
+
+# Download and install Patchwork
+git clone 'https://github.com/fethalen/patchwork' \
+&& cd patchwork/build \
+&& ./build_app.jl
+
+# Stage 2/2: Production
+# ---------------------
+
+# Set the base image
+%environment
+export DEBIAN_FRONTEND=noninteractive
+export TZ=Europe/Zurich
+export PATH="/opt/julia-1.9.3/bin:${PATH}"
+
+Bootstrap: docker
+From: ubuntu:22.04 
+Stage: production
+
+%files from builder
+/opt/patchwork/build/compiled /opt/patchwork
+/usr/local/bin/diamond /usr/local/bin/diamond
+%labels
+org.opencontainers.image.authors="[email protected]"
+version="1"
+software="Patchwork"
+software.version="0.5.4"
+about.author="Felix Thalén <[email protected]>"
+about.summary="Alignment-based Exon Retrieval and Concatenation with Phylogenomic Applications"
+about.home="https://github.com/fethalen/patchwork"
+about.documentation="https://github.com/fethalen/patchwork#readme"
+about.license="SPDX:GPL-3.0"
+about.tags="phylogenomics, phylogenetics, genomics, alignment"
+%post
+
+# Metadata
+
+# System is non-interactive when building the Docker image
+DEBIAN_FRONTEND=noninteractive
+
+# Set time zone to Zurich, Europe
+TZ=Europe/Zurich
+ln -snf "/usr/share/zoneinfo/${TZ}" /etc/localtime && echo "$TZ" > /etc/timezone
+
+# Create the user
+useradd --create-home --shell /bin/bash --user-group --uid 1000 patchwork
+
+# Set the default user
+su -  patchwork # USER patchwork
+
+# Set the working directory
+mkdir -p /home/patchwork
+cd /home/patchwork
+
+PATH=/opt/patchwork/bin:$PATH
+
+%environment
+export DEBIAN_FRONTEND=noninteractive
+export TZ=Europe/Zurich
+export PATH=/opt/patchwork/bin:$PATH
+%runscript
+cd /home/patchwork
+exec patchwork "$@"
+%startscript
+cd /home/patchwork
+exec patchwork "$@"

src/Patchwork.jl

@@ -199,7 +199,7 @@ function parse_parameters()
     whole-genome sequencing data
     """
     settings = ArgParseSettings(description = overview,
-        version = "0.5.4",
+        version = "0.5.5",
         add_version = true)
     @add_arg_table! settings begin
         "--contigs"