安装基因组组装软件DipAsm

DipAsm 是一个利用HiFi数据和Hi-C数据，不需要亲本信息而组装出单倍型的软件。

• 安装

mkdir -p dipasm
cd dipasm
git clone https://github.com/shilpagarg/DipAsm.git
cd DipAsm/docker
docker build -t dipasm .
cd ../../..
docker run -it --rm -v $PWD/dipasm/DipAsm:/wd/dipasm/DipAsm/ -e HOSTWD=$PWD/dipasm/DipAsm -v /var/run/docker.sock:/var/run/docker.sock dipasm:latest /bin/bash

到这一步报错

Unable to find image 'dipasm:latest' locally
docker: Error response from daemon: pull access denied for dipasm, repository does not exist or may require 'docker login': denied: requested access to the resource is denied.
See 'docker run --help'.

尝试解决
1.去docker官网注册账号

#登陆账号
docker  login
#输入用户名和密码

2. 解决"Unable to find image 'dipasm:latest' locally"问题

#查看本地是不是没有dipasm
docker images #确实没有
#查看docker中没有dipasm
docker search dipasm 
#结果
NAME                 DESCRIPTION   STARS     OFFICIAL   AUTOMATED
luhancheng/dipasm                  1                    
grpiccoli/dipasm                   0                    
hpcbiotools/dipasm                 0                    
oldzhg/dipasm                      0      
#从docke中拉取 grpiccoli/dipasm
docker pull grpiccoli/dipasm
#再次查看
docker images  #已有
- 再次运行
docker run -it --rm -v $PWD/dipasm/DipAsm:/wd/dipasm/DipAsm/ -e HOSTWD=$PWD/dipasm/DipAsm -v /var/run/docker.sock:/var/run/docker.sock grpiccoli/dipasm:latest /bin/bash
#成功进入镜像
root@242156fa4e11:

• 运行脚本并查看参数

#进入/wd/dipasm/DipAsm
cd /wd/dipasm/DipAsm
#运行
python pipeline.py -h
#结果
usage: pipeline.py [-h] --hic-path PATH --pb-path PATH --sample NAME [--female] --prefix STR

optional arguments:
  -h, --help       show this help message and exit
  --hic-path PATH  Use Hi-C data from this path. Should be named by *1.fastq and *2.fastq.
  --pb-path PATH   Use PacBioCCS data from this path. All fastq will be used.
  --sample NAME    Sample name to put for Read Group of BAM and Sample of VCF.
  --female         When sample is a female, specify this to also do phasing on chrX.
  --prefix STR     Prefix name for the experiment, for example "refBased", "ragooBased".

• 测试软件中的test数据

cd /wd/dipasm/DipAsm
bash test.sh | bash

再次报错

Unable to find image 'gcr.io/deepvariant-docker/deepvariant:0.8.0' locally
docker: Error response from daemon: Get "https://gcr.io/v2/": net/http: request canceled while waiting for connection (Client.Timeout exceeded while awaiting headers).
See 'docker run --help'.

尝试解决报错

#退出docker镜像
exit
docker image pull google/deepvariant
#重新用拉取 luhancheng/dipasm
docker pull luhancheng/dipasm:39d24cf
docker run -it --rm -v $PWD/dipasm/DipAsm:/wd/dipasm/DipAsm/ -e HOSTWD=$PWD/dipasm/DipAsm -v /var/run/docker.sock:/var/run/docker.sock luhancheng/dipasm:39d24cf /bin/bash
还是报错

卒
重新尝试

docker build -t dipasm .
#运行完以后
Successfully built 0627095308f2
Successfully tagged dipasm:latest
#感觉可以了
docker run -it --rm -v $PWD/dipasm/DipAsm:/wd/dipasm/DipAsm/ -e HOSTWD=$PWD/dipasm/DipAsm -v /var/run/docker.sock:/var/run/docker.sock dipasm:latest /bin/bash

可以进入镜像，成功
#尝试测试数据
cd /wd/dipasm/DipAsm
mkdir -p hi-c; cp tests/hic_* hi-c/
mkdir -p pacbioccs; cp tests/hifi.fastq pacbioccs/
conda activate whdenovo
python pipeline.py --hic-path hi-c --pb-path pacbioccs --sample test --prefix out

难怪这个软件少用，现在已有新的且安装友好的软件hifiasm
chhylp123/hifiasm: Hifiasm: a haplotype-resolved assembler for accurate Hifi reads (github.com)