Apptainer Definition Files

Apptainer定义文件（简称“def文件”）就像一组蓝图，解释如何构建自定义容器。它包括有关要构建的基本操作系统或要开始的基本容器的详细信息、要安装的软件、要在运行时设置的环境变量、要从主机系统添加的文件以及容器元数据。

Apptainer定义文件分为两部分：Header和Sections

Header

Bootstrap: docker
From: ubuntu:20.04

Preferred bootstrap agents

• docker (images hosted on Docker Hub)
• oras (images from supporting OCI registries)
• localimage (images saved on your machine)
• scratch (a flexible option for building a container from scratch)

Other bootstrap agents

• library (images hosted on Library API Registries)
• shub (images hosted on Singularity Hub)
• yum (yum based systems such as CentOS and Scientific Linux)
• debootstrap (apt based systems such as Debian and Ubuntu)
• oci (bundle compliant with OCI Image Specification)
• oci-archive (tar files obeying the OCI Image Layout Specification)
• docker-daemon (images managed by the locally running docker daemon)
• docker-archive (archived docker images)
• arch (Arch Linux)
• busybox (BusyBox)
• zypper (zypper based systems such as Suse and OpenSuse)

Sections

Bootstrap: docker
From: ubuntu:18.04
Stage: build

%setup
    touch /file1
    touch ${APPTAINER_ROOTFS}/file2

%files
    /file1
    /file1 /opt

%environment
    export LISTEN_PORT=12345
    export LC_ALL=C

%post
    apt-get update && apt-get install -y netcat
    NOW=`date`
    echo "export NOW=\"${NOW}\"" >> $APPTAINER_ENVIRONMENT

%runscript
    echo "Container was created $NOW"
    echo "Arguments received: $*"
    exec echo "$@"

%startscript
    nc -lp $LISTEN_PORT

%test
    grep -q NAME=\"Ubuntu\" /etc/os-release
    if [ $? -eq 0 ]; then
        echo "Container base is Ubuntu as expected."
    else
        echo "Container base is not Ubuntu."
        exit 1
    fi

%labels
    Author alice
    Version v0.0.1

%help
    This is a demo container used to illustrate a def file that uses all
    supported sections.

conda activate your_env
conda env export > environment.yml

Bootstrap: docker

From: continuumio/miniconda3

%files
    environment.yml

%post
    /opt/conda/bin/conda env create -f environment.yml

%runscript
    exec /opt/conda/envs/$(head -n 1 environment.yml | cut -f 2 -d ' ')/bin/"$@"

sudo singularity build conda.sif Singularity

singularity run conda.sif ipython

参考: https://apptainer.org/docs/user/main/definition_files.html#