转录组分析-docker镜像安装使用-hisate2 的docker镜像

生信相关工具的镜像文件

https://www.omicsclass.com/article/1245

$ docker search omicsclass
NAME                           DESCRIPTION                                     STARS               OFFICIAL            AUTOMATED
omicsclass/gene-family         gene-family analysis docker image               2
omicsclass/isoseq3             isoseq3 v3.3.0 build by omicsclass              0
omicsclass/bwa                 BWA v0.7.17 build by omicsclass                 0
omicsclass/rnaseq              RNA-seq analysis docker image build by omics…   0
omicsclass/samtools            samtools v1.10 build by omicsclass              0
omicsclass/biocontainer-base   Biocontainers base Image centos7                0
omicsclass/blast-plus          blast+ v2.9.0                                   0
omicsclass/blastall            legacy blastall v2.2.26                         0
omicsclass/sratoolkit          SRAtoolkit v2.10.3 and aspera v3.9.9.177872     0

安装docker

学会安装docker之后，想把转录组分析需要的所有软件都装上，后来发现没这个必要

需要一个难以安装成功的软件的时候，我们再去使用docker镜像即可
保持一个软件，一个docker的简洁

安装成功，主要是3步
参考教程

1. 安装依赖包

sudo apt-get install \
    apt-transport-https \
    ca-certificates \
    curl \
    gnupg-agent \
    software-properties-common

2. 添加密钥

curl -fsSL https://mirrors.ustc.edu.cn/docker-ce/linux/ubuntu/gpg | sudo apt-key add -

3. 官方脚本自动安装

curl -fsSL https://get.docker.com | bash -s docker --mirror Aliyun

安装成功之后显示如下内容:

+ sudo -E sh -c 'DEBIAN_FRONTEND=noninteractive apt-get install -y -qq docker-ce-rootless-extras >/dev/null'
+ sudo -E sh -c 'docker version'
Client: Docker Engine - Community
 Version:           20.10.8
 API version:       1.41
 Go version:        go1.16.6
 Git commit:        3967b7d
 Built:             Fri Jul 30 19:54:08 2021
 OS/Arch:           linux/amd64
 Context:           default
 Experimental:      true

Server: Docker Engine - Community
 Engine:
  Version:          20.10.8
  API version:      1.41 (minimum version 1.12)
  Go version:       go1.16.6
  Git commit:       75249d8
  Built:            Fri Jul 30 19:52:16 2021
  OS/Arch:          linux/amd64
  Experimental:     false
 containerd:
  Version:          1.4.9
  GitCommit:        e25210fe30a0a703442421b0f60afac609f950a3
 runc:
  Version:          1.0.1
  GitCommit:        v1.0.1-0-g4144b63
 docker-init:
  Version:          0.19.0
  GitCommit:        de40ad0

================================================================================

To run Docker as a non-privileged user, consider setting up the
Docker daemon in rootless mode for your user:

    dockerd-rootless-setuptool.sh install

Visit https://docs.docker.com/go/rootless/ to learn about rootless mode.


To run the Docker daemon as a fully privileged service, but granting non-root
users access, refer to https://docs.docker.com/go/daemon-access/

WARNING: Access to the remote API on a privileged Docker daemon is equivalent
         to root access on the host. Refer to the 'Docker daemon attack surface'
         documentation for details: https://docs.docker.com/go/attack-surface/

================================================================================

测试docker是否安装成功 - 容器内运行程序

https://www.runoob.com/docker/docker-hello-world.html

教程效果

本地测试效果

1. 命令

docker run ubuntu:15.10 /bin/echo "Hello world"

2. 如果这个镜像ubuntu:15.10不存在，则下载它
3. 执行命令 /bin/echo "Hello world"，输出内容

测试docker是否安装成功 - 运行交互式的容器

通过 docker 的两个参数 -i -t，让 docker 运行的容器实现"对话"的能力

$ docker run -i -t ubuntu:15.10 /bin/bash
root@0123ce188bd8:/#

下载并使用安装了 hisat2软件的rna-seq镜像

镜像地址： https://hub.docker.com/r/kathrinklee/rna-seq-pipeline-hisat2

使用

sudo docker run kathrinklee/rna-seq-pipeline-hisat2 hisat2 -h

打印出帮助文档，说明安装成功

下一步计划

把项目需要使用到的docker都打包放在同一个目录下面，方便后期迁移