pVACtool 工具說明文檔Installation — pVACtools 4.0.6 documentation

官網(wǎng)中推薦了兩種安裝方式：
（1）pip install pvactools
（2）docker pull griffithlab/pvactools
第一種 pip install 折騰了一上午沒有成功，推薦第二種。

用root 權(quán)限 安裝docker，安裝官網(wǎng)推薦步驟，docker
Install Docker Engine on CentOS | Docker Docs

yum remove docker \
                  docker-client \
                  docker-client-latest \
                  docker-common \
                  docker-latest \
                  docker-latest-logrotate \
                  docker-logrotate \
                  docker-engine

yum install -y yum-utils
yum-config-manager --add-repo https://download.docker.com/linux/centos/docker-ce.repo  

 yum install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
##這一步會出現(xiàn)error

##由于鏡像網(wǎng)速的問題，切換為阿里鏡像
yum-config-manager --add-repo  https://mirrors.aliyun.com/docker-ce/linux/centos/docker-ce.repo 
##重復(fù)執(zhí)行下面這一步
yum install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
## 提示error：  Requires: fuse-overlayfs ＞= 0.7 等。。
yum install fuse-overlayfs  container-selinux  slirp4netns
## 提示當(dāng)前鏡像中沒有找到 fuse-overlayfs package.
## 百度后通過修改  /etc/yum.repos.d/docker-ce.repo 
vim /etc/yum.repos.d/docker-ce.repo
[centos-extras]
name=Centos extras - $basearch
baseurl=http://mirror.centos.org/centos/7/extras/x86_64
enable=1
gpgcheck=0
## 重新執(zhí)行，成功
yum install fuse-overlayfs  container-selinux  slirp4netns   
yum install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin # 安裝成功

$ docker --version
$ Docker version 24.0.7, build afdd53b   #當(dāng)前docker  版本號

## 添加docker 用戶組，否則普通用戶無法使用
groupadd docker    # docker group 默認(rèn)已經(jīng)生成，不放心可以執(zhí)行一遍
gpasswd -a $USER docker  #將所有用戶加到docker group
newgrp docker  #更新

#啟動docker 
systemctl start docker
# 嘗試 pull 鏡像
docker pull griffithlab/pvactools
docker images  #可以看到鏡像
REPOSITORY              TAG       IMAGE ID       CREATED        SIZE
griffithlab/pvactools   latest    981a3b8b2bd8   4 months ago   9.18GB
hello-world             latest    d2c94e258dcb   8 months ago   13.3kB

pVACtools模塊pvacseq 的input 需要VEP 注釋，下一步安裝VEP
按照ensemble VEP 官方文檔安裝 Download and install (ensembl.org)

git clone https://github.com/Ensembl/ensembl-vep.git  #git 非常依賴網(wǎng)速，可以多嘗試幾次
cd ensembl-vep
perl INSTALL.pl  # 需要的perl 包都已經(jīng)在INSTALL.pl 中，直接執(zhí)行即可。這一步也非常依賴網(wǎng)速，可以多嘗試幾次。 會生成./Bio 文件夾
#安裝成功，會出現(xiàn)提示 “Testing VEP installation -OK!” ，如下面
###############VEP ########################
[root@master ensembl-vep]# perl INSTALL.pl --NO_HTSLIB 
curl failed (000), trying to fetch using LWP::Simple
LWP::Simple failed (501), trying to fetch using HTTP::Tiny
Hello! This installer will help you set up VEP v110, including:
 - Install v110 of the Ensembl API for use by the VEP. It will not affect any existing installations of the Ensembl API that you may have.
 - Download and install cache files from Ensembl's FTP server.
 - Download FASTA files from Ensembl's FTP server.
 - Download VEP plugins.

Checking for installed versions of the Ensembl API...done

Setting up directories
Destination directory ./Bio already exists.
Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? y
 - fetching BioPerl
 - unpacking ./Bio/tmp/release-1-6-924.zip
 - moving files

Downloading required Ensembl API files
 - fetching ensembl
 - unpacking ./Bio/tmp/ensembl.zip
 - moving files
 - getting version information
 - fetching ensembl-variation
 - unpacking ./Bio/tmp/ensembl-variation.zip
 - moving files
 - getting version information
 - fetching ensembl-funcgen
 - unpacking ./Bio/tmp/ensembl-funcgen.zip
 - moving files
 - getting version information
 - fetching ensembl-io
 - unpacking ./Bio/tmp/ensembl-io.zip
 - moving files
 - getting version information

Testing VEP installation
 - OK!

The VEP can either connect to remote or local databases, or use local cache files.
Using local cache files is the fastest and most efficient way to run the VEP
Cache files will be stored in /root/.vep
Do you want to install any cache files (y/n)? y
Cache directory /root/.vep does not exists - do you want to create it (y/n)? y
 - getting list of available cache files
which: no bgzip in (/share/software/anaconda3/condabin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/root/bin)
which: no tabix in (/share/software/anaconda3/condabin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/root/bin)
The following species/files are available; which do you want (specify multiple separated by spaces or 0 for all): 
1 : acanthochromis_polyacanthus_vep_110_ASM210954v1.tar.gz (69 MB)
2 : accipiter_nisus_vep_110_Accipiter_nisus_ver1.0.tar.gz (54 MB)
...
##################################################################

#下一步會開始下載VEP 的databases，這一步可以另外自行下載，文件比較的大，網(wǎng)速慢
#利用提示中的網(wǎng)址，復(fù)制下載鏈接，VEP 不同版本對應(yīng)不用數(shù)據(jù)庫版本
#在提示下載的時候，選一個文件，這樣方便看當(dāng)前VEP 依賴的databases FTP 路徑
# human hg38  -110
https://ftp.ensembl.org/pub/release-110/variation/vep/homo_sapiens_merged_vep_110_GRCh38.tar.gz
https://ftp.ensembl.org/pub/release-110/variation/vep/homo_sapiens_refseq_vep_110_GRCh38.tar.gz
https://ftp.ensembl.org/pub/release-110/variation/vep/homo_sapiens_vep_110_GRCh38.tar.gz

docker /VEP / pvactools 都成功后，下一步測試pvactools 的模塊~~ 明天繼續(xù)