Docker运行科研工具
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内容来自：Genomics in the Cloud_ Using Docker, GATK, and WDL in Terra
//Docker安装 ubuntu18.04
$ curl -sSL https://get.docker.com/ | shExecuting docker install script, commit: f45d7c11389849ff46a6b4d94e0dd1ffebca
32c1 + sudo -E sh -c apt-get update -qq >/dev/null
...
Client: Docker Engine - Community
Version: 19.03.5
...
If you would like to use Docker as a non-root user, you should now consider
adding your user to the "docker" group with something like:
sudo usermod -aG docker genomics_book
Remember that you will have to log out and back in for this to take effect!
WARNING: Adding a user to the "docker" group will grant the ability to run
containers which can be used to obtain root privileges on the
docker host.
Refer to https://docs.docker.com/engine/security/security/#docker-daemon-
attack-surface for more information.$ sudo usermod -aG docker $USER
docker pull ubuntu
Using default tag: latest
latest: Pulling from library/ubuntu
7413c47ba209: Pull complete
0fe7e7cbb2e8: Pull complete
1d425c982345: Pull complete
344da5c95cec: Pull complete
Digest: sha256:d91842ef309155b85a9e5c59566719308fab816b40d376809c39cf1cf4de3c6a
Status: Downloaded newer image for ubuntu:latest
docker.io/library/ubuntu:latest$ docker run ubuntu
-name=meaningful_name 最好加一个有意义的名字
$ docker run ubuntu echo "Hello World!"
Hello World!$ docker run -it ubuntu /bin/bash
root@d84c079d0623:/#exit 退出
Ctrl+P+Q detach
docker ps -a
//重新连接
docker attach c2b4f8a0c7a6//挂载本地目录
$ docker run -v ~/book:/home/book -it ubuntu /bin/bash
///////////gatk
$ docker pull us.gcr.io/broad-gatk/gatk:4.1.3.0
4.1.3.0: Pulling from us.gcr.io/broad-gatk/gatk
ae79f2514705: Pull complete
5ad56d5fc149: Pull complete
170e558760e8: Pull complete
395460e233f5: Pull complete
6f01dc62e444: Pull complete
b48fdadebab0: Pull complete
16fb14f5f7c9: Pull complete
Digest: sha256:e37193b61536cf21a2e1bcbdb71eac3d50dcb4917f4d7362b09f8d07e7c2ae50
Status: Downloaded newer image for us.gcr.io/broad-gatk/gatk:4.1.3.0
us.gcr.io/broad-gatk/gatk:4.1.3.0$ docker run -v ~/book:/home/book -it us.gcr.io/broad-gatk/gatk:4.1.3.0 /bin/bash
//通过IGV查看突变
