BD Rhapsody单细胞分析系统

Create: Yuan.Sh
Date: 2022-08-29 10:42:56
E-mail: yuansh3354@163.com
Blog: https://blog.csdn.net/qq_40966210
Add: Fujian Medical University
SUM: BD 单细胞测序上游流程 官方指导文件
Ref: https://www.nature.com/articles/s41592-018-0255-0#Sec2

配置 Docker

根据官方文件描述，BD上游分析有两种方法，第一种是根据七桥基因平台注册，但是注册方法太麻烦了，就暂时不考虑这个方法。第二种是使用Docker进行本地运行

Docker 官方安装指南

proxy_on
sudo apt-get update

sudo apt-get install \
    ca-certificates \
    curl \
    gnupg \
    lsb-release

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg

echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \
  $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null

sudo apt-get install docker-ce docker-ce-cli containerd.io docker-compose-plugin、

apt-cache madison docker-ce
# 这时候系统会输出最新的版本
# docker-ce | 5:20.10.17~3-0~ubuntu-focal | https://download.docker.com/linux/ubuntu focal/stable amd64 Packages

# 使用最新版本号（ 5:20.10.17~3-0~ubuntu-focal）替换（<VERSION_STRING>）
sudo apt-get install docker-ce=<VERSION_STRING> docker-ce-cli=<VERSION_STRING> containerd.io docker-compose-plugin

# 修改权限
sudo chmod 666 /var/run/docker.sock
sudo usermod -aG docker ${USER}

下载储存库文件和参考数据

链接地址：https://bitbucket.org/CRSwDev/cwl/downloads/

wget -c https://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-WTA/GRCm38-PhiX-gencodevM19/GRCm38-PhiX-gencodevM19-20181206.tar.gz
wget -c https://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-WTA/GRCm38-PhiX-gencodevM19/gencodevM19-20181206.gtf

安装CWL-tool

因为我使用的是 conda 环境所以python就不用安装了
直接安装cwl-runner

pip install cwlref-runner
sudo apt install nodejs
# check 
cwl-runner

设置配置文件

打开刚刚下载的储存库文件（就是刚刚下载的CRS.zip），然后选择最新版本的文件夹里的配置文件，我用的是1.9.1

# 备份一下配置文件
cp template_wta_1.9.1.yml my_wta_1.9.1-2022-08-29_11-57.yml

修改配置文件为如下

#!/usr/bin/env cwl-runner

cwl:tool: rhapsody

# This is a template YML file used to specify the inputs for a BD Genomics WTA Rhapsody Analysis pipeline run. See the
# BD Genomics Analysis Setup User Guide (Doc ID: 47383) for more details. Enter the following information:


## Reads (required) - Path to your read files in the FASTQ.GZ format. You may specify as many R1/R2 read pairs as you want.
Reads:

 - class: File
   location: "S1_R1.fastq.gz"
 - class: File
   location: "S1_R2.fastq.gz"

 - class: File
   location: "S2_R1.fastq.gz"
 - class: File
   location: "S2_R2.fastq.gz"

 - class: File
   location: "S3_R1.fastq.gz"
 - class: File
   location: "S3_R2.fastq.gz"

## Reference_Genome (required) - Path to STAR index for tar.gz format. See Doc ID: 47383 for instructions to obtain pre-built STAR index file.
Reference_Genome:
   class: File
   location: "ref/GRCm38-PhiX-gencodevM19-20181206.tar.gz"

## Transcriptome_Annotation (required) - Path to GTF annotation file
Transcriptome_Annotation:
   class: File
   location: "ref/gencodevM19-20181206.gtf"

Sample_Tags_Version: mouse # 我的数据是老鼠的数据，如果是人的设置为humman即可
Tag_Names: [L-AFLD, L-CON, L-Fibrosis, L-NAFLD, T-AFLD, T-CON, T-Fibrosis, T-NAFLD]

执行分析流程

进入刚刚的1.9.1的文件夹下面

cwl-runner --outdir /media/yuansh/14THHD/WQ/scRNA-out rhapsody_wta_1.9.1.cwl my_wta_1.9.1-2022-08-29_11-57.yml