snakemake流程-CellChat

[zhanglu]

#########################
python3.8 r4.0.5

注意安装过程有包需要更新，选择不更新， 更新后会相互影响

conda install -c conda-forge r-base==4.0.5 -y
conda install r-stringi r-stringr r-devtools -y -c conda-forge
install.packages("BiocManager",repos="https://mirrors.tuna.tsinghua.edu.cn/CRAN/")
BiocManager::install('Biobase')

install.packages("NMF", repos='https://mirrors.tuna.tsinghua.edu.cn/CRAN/')
install.packages('memoise', repos='https://mirrors.tuna.tsinghua.edu.cn/CRAN/')
install.packages('processx', repos='https://mirrors.tuna.tsinghua.edu.cn/CRAN/')
install.packages("circlize", repos='https://mirrors.tuna.tsinghua.edu.cn/CRAN/')
devtools::install_github("jokergoo/ComplexHeatmap")
pip install umap-learn -i https://pypi.tuna.tsinghua.edu.cn/simple
devtools::install_github("sqjin/CellChat")
install.packages("optparse", repos='https://mirrors.tuna.tsinghua.edu.cn/CRAN/')

安装CellChat时，会有一下依赖问题；

install.packages("statnet.common", repos='https://mirrors.tuna.tsinghua.edu.cn/CRAN/')
2: In i.p(...) :
installation of package ‘statnet.common’ had non-zero exit status
3: In i.p(...) :
installation of package ‘stringi’ had non-zero exit status
4: In i.p(...) : installation of package ‘car’ had non-zero exit status
5: In i.p(...) :
installation of package ‘network’ had non-zero exit status
6: In i.p(...) :
installation of package ‘rstatix’ had non-zero exit status
7: In i.p(...) : installation of package ‘sna’ had non-zero exit status
8: In i.p(...) : installation of package ‘ggpubr’ had non-zero exit status
9: In i.p(...) :
installation of package ‘ggnetwork’ had non-zero exit status

conda install -c conda-forge r-statnet.common
conda install -c conda-forge r-stringi r-pbkrtest
conda install -c conda-forge r-sna r-ggpubr r-ggnetwork r-rstatix
BiocManager::install("BiocNeighbors")

devtools::install_github("sqjin/CellChat")

install.packages("optparse", repos='https://mirrors.tuna.tsinghua.edu.cn/CRAN/')
pip install anndata -i https://pypi.tuna.tsinghua.edu.cn/simple

运行命令：
snakemake -s workflow/Snakefile --configfile config/config.yaml --cores 8
Rscript workflow/scripts/run_cellchat.R -i /home/genostack/workspace/ms_jk_small_tool/cellchat_tmp/code/setCelltypeCategories.h5ad -s hsapiens -g cell_type_main --PPI_use False --nmultiprocess 20 --annotation_use NULL --n_top 10 -o results 2>&1 >logs/run_cellchat.log

[zhanglu]

https://github.com/sqjin/CellChat