通过conda安装纯净环境的CellChat

发布于 2022-03-12  300 次阅读


  • https://anaconda.org/conda-forge/r-base
  • conda create -n cellchat -c conda-forge r-base=4.1.2 -y
  • conda activate cellchat
  • conda install -c conda-forge r-seurat=4.1.0 -y
  • conda install -c conda-forge r-irkernel=1.3 -y
  • conda install -c conda-forge r-biocmanager=1.30.16 -y
  • conda install -c conda-forge r-devtools=2.4.3 -y
  • conda install -c conda-forge r-circlize=0.4.14 -y
  • conda install -c conda-forge umap-learn=0.5.3 -y
  • conda install -c bioconda bioconductor-biobase=2.54.0 -y
  • wget https://github.com/sqjin/CellChat/archive/refs/heads/master.zip -O CellChat-master.zip
  • 移除CellChat-master.zip里src目录下的*.so和*.o文件
  • unzip CellChat-master.zip
  • rm CellChat-master/src/*.so
  • rm CellChat-master/src/*.o
  • wget https://github.com/jokergoo/ComplexHeatmap/archive/refs/heads/master.zip -O ComplexHeatmap-master.zip
  • conda install -c conda-forge r-svglite=2.1.0 -y
  • install.packages('NMF')
  • devtools::install_local('ComplexHeatmap-master.zip')
  • devtools::install_local('CellChat-master')
  • IRkernel::installspec(name='cellchat', displayname='r-cellchat')
Sys.setenv(RETICULATE_PYTHON = "/opt/conda/envs/cellchat/bin/python3.7")
library('reticulate')
use_condaenv("cellchat")
py_config()

 


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