使用mamba替換miniconda和anaconda，原因是速度更快，無論是創(chuàng)建新環(huán)境還是激活環(huán)境

conda、mamba、anaconda都是蟒蛇的意思…

下載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使用命令行下載mambaforge

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

windows版本和linux、mac版本可以從夸克網盤下載
鏈接：https://pan.quark.cn/s/6fd066275bd1
提取碼：iG2E

安裝

windows直接鼠標雙擊打開Mambaforge-Windows-x86_64.exe文件在圖形界面安裝；

linux和mac在命令行中安裝

bash Mambaforge*.sh

• 設置鏡像

linux和mac在${HOME}目錄下新建文件.condarc

Windows中默認路徑為C:\Users\用戶名\.condarc

always_yes設為true， 也不用每次加-y參數或者每次手動輸入y確認安裝包了。

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/

創(chuàng)建一個簡單環(huán)境

創(chuàng)建一個名叫fastq_env的環(huán)境，包括一個軟件fastqc

mamba create -n fastq_env -c bioconda fastqc

創(chuàng)建一個單細胞分析環(huán)境

示例創(chuàng)建一個Python單細胞分析環(huán)境；

• SC.yml文件如下

name 是環(huán)境名，prefix為環(huán)境目錄路徑，channels為鏡像文件.condarc中設置的國內鏡像名；dependencies包及其版本號

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

• 創(chuàng)建環(huán)境

mamba env create -f SC.yml

創(chuàng)建一個R單細胞環(huán)境

R.yml文件如下，包括R4.3.2、tidyverse系列數據處理軟件

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

• 創(chuàng)建環(huán)境

mamba env create -f R.yml

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