[tools] docker & singularity

command

docker ps 查看现在运行的docker

docker exec -it [name] 运行

docker stop [name] 停止运行

sudo chown -R $USER:$USER . 有的时候docker会让一些folder失去permission，这个时候change owner (chown)， -R是recursive，后面跟着新的user

notes

每次打开terminal可以： sudo apt-get update

如果sudo apt install package失败，可以sudo apt --fix-broken install，然后再重新install。

Docker

build docker

docker build -t my-image -f docker/Dockerfile .

-t (tag): 给image一个name和optionally一个version tag，比如my-image:1.0,或者之际my-image，会默认为my-image:latest

-f (file): docker file位置

. : 指定build directory

push to DockerHub

docker login

docker tag my-image myusername/myrepo

docker push myusername/myrepo

如果只想要一个docker的环境，可以把CMD行（如果有的话）取消掉，然后再上传。

optional: 在myusername/myrepo后加:version-tag

Singularity

安装

先查看自己ubuntu系统的version，再找对应的version

lsb_release -a

• focal Ubuntu 20.04.
• jammy Ubuntu 22.04.

进入singularity github release https://github.com/sylabs/singularity/releases

根据系统focal还是jammy,找到相应的deb，复制链接。

wget link

下载好之后，sudo dpkg --install 【file.deb】

然后， sudo apt-get install -yf

查看版本：singularity --version

使用

build

cd alphafold3
docker build -t alphafold3 -f docker/Dockerfile .

docker run -d -p 5000:5000 --restart=always --name registry registry:2
docker tag alphafold3 localhost:5000/alphafold3
docker push localhost:5000/alphafold3

# NO HTTPS indicate that this is localhost, not from http
SINGULARITY_NOHTTPS=1 singularity build alphafold3.sif docker://localhost:5000/alphafold3:latest

Run

singularity exec --nv alphafold3.sif \
python -u alphafold3/run_alphafold.py \
--input_dir=af_input_ECD_Immunoglobulin/folder_3 \
--model_dir=af_models \
--output_dir=af_output_ECD_Immunoglobulin \
--norun_data_pipeline | tee run.log

Apptainer

install

check https://github.com/apptainer/apptainer/blob/main/INSTALL.md

apt-get update
apt-get install -y \
    build-essential \
    libseccomp-dev \
    pkg-config \
    uidmap \
    squashfs-tools \
    fakeroot \
    cryptsetup \
    tzdata \
    dh-apparmor \
    curl wget git

check .deb files in release https://github.com/apptainer/apptainer/releases

get latest version, download through wget

wget link
dpkg -i apptainer_1.3.5_amd64.deb
apt-get install -f

if any of not work, use (with or without sudo)

sudo apt --fix-broken install
sudo apt update
sudo apt upgrade

build from docker

apptainer build af3.sif docker://cford38/alphafold3

build from local .def file

apptainer build af3.sif singularity.def