通过conda安装纯净环境的 Monocle3

发布于 2022-03-12  339 次阅读


  • conda create -n monocle3 -c conda-forge r-base=4.1.2 -y
  • conda activate monocle3
  • 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 bioconda bioconductor-limma=3.50.1 -y
  • conda install -c bioconda bioconductor-summarizedexperiment=1.24.0 -y
  • conda install -c bioconda bioconductor-batchelor=1.10.0 -y
  • conda install -c bioconda bioconductor-biocparallel=1.28.3 -y
  • conda install -c conda-forge r-doparallel=1.0.17 -y
  • conda install -c conda-forge parallel=20220222 -y
  • conda install -c conda-forge r-foreach=1.5.2 -y
  • conda install -c conda-forge r-matrix.utils=0.9.8 -y
  • conda create -n cytoTRACE -c conda-forge python=3.7 -y
  • conda activate cytoTRACE
  • conda install -c conda-forge numpy -y
  • /opt/conda/envs/cytoTRACE/bin/pip3 install scanoramaCT -i https://pypi.tuna.tsinghua.edu.cn/simple
  • conda deactivate
  • wget https://cytotrace.stanford.edu/CytoTRACE_0.3.3.tar.gz -O CytoTRACE_0.3.3.tar.gz
  • conda install -c conda-forge r-sf=1.0_6 -y
  • wget https://github.com/cole-trapnell-lab/leidenbase/archive/refs/heads/master.zip -O leidenbase-master.zip
  • wget https://github.com/cole-trapnell-lab/monocle3/archive/refs/heads/master.zip -O monocle3-master.zip
  • conda install -c bioconda bioconductor-sva=3.42.0 -y
  • conda install -c conda-forge r-ggpubr=0.4.0 -y
  • conda install -c conda-forge r-spdep=1.2_2 -y
  • devtools::install_local("CytoTRACE_0.3.3.tar.gz")
  • devtools::install_local("leidenbase-master.zip")
  • devtools::install_local("monocle3-master.zip")
  • BiocManager::install(c("DDRTree", "monocle"))
  • IRkernel::installspec(name='monocle3', displayname='r-monocle3')
library(reticulate)
use_condaenv("cytoTRACE")

 


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