【宏基因组】metaWRAP安装记录

metaWRAP安装记录

需要metawrap做binning，光是安装依赖项就花了很长时间，最后终于成功了，来之不易。

metawrap指出【安装和管理metaWRAP最好的方法是直接从github安装，然后通过conda安装它的所有依赖】，但是conda安装报错频频，我为了更换mamba用于快速安装，下载了miniforge。

1. 本体

git clone https://github.com/bxlab/metaWRAP.git
vim ~/.bash_profile 
### 添加PATH=yourpath/metaWRAP/bin/:$PATH到~/.bash_profile 
source ~/.bash_profile

2. 依赖项

# 新建环境
conda create -y -n metawrap python=2.7
conda activate metawrap
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels ursky

# 下载并安装miniforge
wget -c --no-check-certificate --no-cookies --header "Cookie: oraclelicense=accept-securebackup-cookie" https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh
### 同意协议，我之后安装在了默认目录/home/DE/的miniforge3文件夹内

# 使用miniforge里的mamba安装metawrap的依赖项
# 根据了官网给出的依赖项内容
path=yourpath/miniforge3/bin
${path}/mamba install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore concoct

# 最后输出结果是 提示运行以下命令获取一些库
# The default QUAST package does not include:
# * GRIDSS (needed for structural variants detection)
# * SILVA 16S rRNA database (needed for reference genome detection in metagenomic datasets)
# * BUSCO tools and databases (needed for searching BUSCO genes) -- works in Linux only!
# To be able to use those, please run
    quast-download-gridss
    quast-download-silva
    quast-download-busco

# checkM 数据库配置
# sudo checkm data update或https://data.ace.uq.edu.au/public/CheckM_databases/查找数据库文件下载、解压。
wget -c --no-check-certificate --no-cookies --header "Cookie: oraclelicense=accept-securebackup-cookie" https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar -xvf checkm_data_2015_01_16.tar.gz
checkm data setRoot yourdatabase/checkM/ # 设置数据库路径

完成！
mamba真好用，感谢miniforge！（抹眼泪）