Definition file for an Apptainer container

README.md

@@ -50,6 +50,29 @@ sudo apt update
 sudo apt install jellyfish
 ```
 
+### Apptainer container
+
+From the git repository, create a container image (`jellyfish.sif` file) with:
+
+``` Shell
+apptainer build jellyfish.sif jellyfish.def
+```
+
+By default it builds the code from the `HEAD` branch of the git repository.
+This can be change using the `treeish` build argument.
+For example, to build version 2.3.1:
+``` Shell
+apptainer build --build-arg treeish=v2.3.1 jellyfish.sif jellyfish.def
+```
+
+The default command is the `jellyfish` command.
+Use like this:
+``` Shell
+apptainer run jellyfish.sif count -m 21 -C -s 10M -o output.jf input.fa
+```
+
+Get some help with `apptainer run-help jellyfish.sif`
+
 ### From source
 
 To get an easier to compiled packaged tar ball of the source code, download a release from the [github release][3]. You need make and g++ version 4.4 or higher. To install in your home directory, do:

jellyfish.def

@@ -0,0 +1,64 @@
+Bootstrap: docker
+From: ubuntu:22.04
+Stage: devel
+
+%arguments
+    # Branch to build
+    treeish=HEAD
+
+%setup
+    mkdir -p ${APPTAINER_ROOTFS}/usr/local/src/jellyfish
+    git archive {{ treeish }} | tar -x -C ${APPTAINER_ROOTFS}/usr/local/src/jellyfish
+
+%post
+    # System installations
+    apt update
+    apt install -y --no-install-recommends yaggo build-essential autoconf automake libtool gettext pkg-config swig python3-dev libperl-dev ruby-dev
+
+    # Build and install
+    cd /usr/local/src/jellyfish
+    autoreconf -fi
+    PVERSION=$(python3 -V | grep -Po '\b[\d.]+\b' | cut -d. -f1-2)
+    ./configure --enable-swig --enable-all-binding PYTHON_VERSION="$PVERSION"
+    make -j`nproc`
+    make install DESTDIR=$(pwd)/inst
+
+
+Bootstrap: docker
+From: ubuntu:22.04
+Stage: final
+
+%help
+    By default runs the jellyfish command. See --help for help.
+    If the first argument is "python", "perl", "ruby" or "irb", run
+    these commands. The Jellyfish module (called "jellyfish" for Perl
+    and Ruby, but "dna_jellyfish" for Python) is available to import/use/require.
+
+%files from devel
+    /usr/local/src/jellyfish/inst/* /
+
+%post
+    ldconfig
+    apt update
+    apt install -y --no-install-recommends python3 perl ruby
+    apt-get clean
+
+%test
+    set -e
+    echo -n "Jellyfish cmd: "; jellyfish --help > /dev/null && echo "Good"
+    echo -n "Python import: "; python3 -c 'import dna_jellyfish; print("Good")'
+    echo -n "Perl use: ";      perl -mjellyfish -e 'print("Good\n")'
+    echo -n "Ruby require: ";  ruby -rjellyfish -e 'puts("Good")'
+
+%runscript
+    #! /bin/bash
+    CMD=("jellyfish")
+    case "$1" in
+      (python) CMD=("python3"); shift ;;
+      (python3) CMD=("python3"); shift ;;
+      (perl) CMD=("perl" "-mjellyfish"); shift ;;
+      (ruby) CMD=("ruby" "-rjellyfish"); shift ;;
+      (irb) CMD=("irb" "-rjellyfish"); shift ;;
+      (jellyfish) shift ;;
+    esac
+    exec "${CMD[@]}" "$@"