使用mamba替换conda和anaconda配置环境安装软件

使用mamba替换miniconda和anaconda，原因是速度更快，无论是创建新环境还是激活环境

conda、mamba、anaconda都是蟒蛇的意思…

下载mambaforge

wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
bash Mambaforge-Linux-x86_64.sh

linux和mac使用命令行下载mambaforge

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"

windows版本和linux、mac版本可以从夸克网盘下载
链接：https://pan.quark.cn/s/6fd066275bd1
提取码：iG2E

安装

windows直接鼠标双击打开Mambaforge-Windows-x86_64.exe文件在图形界面安装；

linux和mac在命令行中安装

bash Mambaforge*.sh

• 设置镜像

linux和mac在${HOME}目录下新建文件.condarc

Windows中默认路径为C:\Users\用户名\.condarc

always_yes设为true， 也不用每次加-y参数或者每次手动输入y确认安装包了。

always_yes: true
show_channel_urls: true
channels:- defaults
default_channels:- https://mirror.sjtu.edu.cn/anaconda/pkgs/r- https://mirror.sjtu.edu.cn/anaconda/pkgs/main
custom_channels:conda-forge: https://mirror.sjtu.edu.cn/anaconda/cloud/pytorch: https://mirror.sjtu.edu.cn/anaconda/cloud/bioconda: https://mirror.sjtu.edu.cn/anaconda/cloud/

创建一个简单环境

创建一个名叫fastq_env的环境，包括一个软件fastqc

mamba create -n fastq_env -c bioconda fastqc

创建一个单细胞分析环境

示例创建一个Python单细胞分析环境；

• SC.yml文件如下

name 是环境名，prefix为环境目录路径，channels为镜像文件.condarc中设置的国内镜像名；dependencies包及其版本号

name: SC
prefix: /home/victor/mambaforge/envs/SC
channels:- conda-forge- bioconda- plotly
dependencies:- python=3.11- numpy- pandas- bioinfokit- matplotlib- seaborn- matplotlib-venn- adjustText- tabulate- textwrap3- notebook- ipykernel- openpyxl- pyarrow- scanpy- python-igraph- leidenalg- pytables- harmonypy- plotly- cython- scikit-learn- python-louvain- pip- pip:- scrublet- celltypist- pyscenic- cell2location- pydeseq2- gseapy

• 创建环境

mamba env create -f SC.yml

创建一个R单细胞环境

R.yml文件如下，包括R4.3.2、tidyverse系列数据处理软件

name: R
prefix: /home/victor/mambaforge/envs/R
channels:- conda-forge- bioconda
dependencies:- r-base=4.3.2- r-monocle3- r-terra- r-tidyverse- r-lme4- r-ggrastr- r-pheatmap- r-plotly- r-gplots- conda-forge:r-seurat- conda-forge:r-seuratobject- conda-forge:r-circlize- conda-forge:r-speedglm- conda-forge:r-htmlwidgets- bioconductor-biocgenerics- bioconductor-delayedarray- bioconductor-delayedmatrixstats- bioconductor-limma- bioconductor-s4vectors- bioconductor-summarizedexperiment- bioconductor-batchelor- bioconductor-hdf5array- bioconductor-complexheatmap- bioconductor-monocle- libgdal- libudunits2

• 创建环境

mamba env create -f R.yml