pVACtool 工具说明文档Installation — pVACtools 4.0.6 documentation
官网中推荐了两种安装方式：
（1）pip install pvactools
（2）docker pull griffithlab/pvactools
第一种 pip install 折腾了一上午没有成功，推荐第二种。
用root 权限 安装docker，安装官网推荐步骤，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
##这一步会出现error
##由于镜像网速的问题，切换为阿里镜像
yum-config-manager --add-repo https://mirrors.aliyun.com/docker-ce/linux/centos/docker-ce.repo
##重复执行下面这一步
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
## 提示当前镜像中没有找到 fuse-overlayfs package.
## 百度后通过修改 /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
## 重新执行，成功
yum install fuse-overlayfs container-selinux slirp4netns
yum install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin # 安装成功
$ docker --version
$ Docker version 24.0.7, build afdd53b #当前docker 版本号
## 添加docker 用户组，否则普通用户无法使用
groupadd docker # docker group 默认已经生成，不放心可以执行一遍
gpasswd -a $USER docker #将所有用户加到docker group
newgrp docker #更新
#启动docker
systemctl start docker
# 尝试 pull 镜像
docker pull griffithlab/pvactools
docker images #可以看到镜像
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模块pvacseq 的input 需要VEP 注释，下一步安装VEP
按照ensemble VEP 官方文档安装 Download and install (ensembl.org)
git clone https://github.com/Ensembl/ensembl-vep.git #git 非常依赖网速，可以多尝试几次
cd ensembl-vep
perl INSTALL.pl # 需要的perl 包都已经在INSTALL.pl 中，直接执行即可。这一步也非常依赖网速，可以多尝试几次。 会生成./Bio 文件夹
#安装成功，会出现提示 “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)
...
##################################################################
#下一步会开始下载VEP 的databases，这一步可以另外自行下载，文件比较的大，网速慢
#利用提示中的网址，复制下载链接，VEP 不同版本对应不用数据库版本
#在提示下载的时候，选一个文件，这样方便看当前VEP 依赖的databases FTP 路径
# 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，下一步测试pvactools 的模块~~ 明天继续
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