单细胞ATAC实战02: 基因组下载和SnapATAC2安装

安装Rust、Fortran、C编译器

可选，如果需要自己编译某些软件则需要安装对应的编译器。

• rust

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
rustup default nightly
source "$HOME/.cargo/env"
# 查看是否安装成功
which cargo

• cmake

brew install cmake
# 查看是否安装成功
which cmake

• gcc

xcode-select --install # Apple M2
brew install gcc
# 查看是否安装成功
which gcc

准备环境Apple M2

brew install --cask mambaforge #Apple M2
mamba create -n ATAC
mamba activate ATAC 
mamba install -y -c conda-forge  python=3.8 cython numpy notebook ipywidgets xgboost scanpy rustworkx polars tenacity pyarrow scvi-tools
mamba install -y -c bioconda harmonypy
mamba install -y -c plotly plotly
pip install SnapATAC2

# Apple 芯片的电脑 的 pytorch 使用gpu需要设置
mamba env config vars set PYTORCH_ENABLE_MPS_FALLBACK=1

which python
# /opt/homebrew/Caskroom/mambaforge/base/envs/ATAC/bin/python

修改源代码的bug

MACS2

这个包的2.2.7.1版本的setup.py源代码中依赖的numpy> => =1.17，因此导致用pip安装的时候报错，所以从github下载2.2.7.1的源码并安装。

wget https://codeload.github.com/macs3-project/MACS/tar.gz/refs/tags/v2.2.7.1
tar -xf MACS-2.2.7.1.tar.gz
cd MACS-2.2.7.1

## 修改setup.py文件
numpy_requires = '>
    =1.17'
install_requires = [f"numpy>
={
numpy_requires}
    ",]
# 改为
numpy_requires = '>
=1.17'
install_requires = [f"numpy{
numpy_requires}
    ",]

# 安装
python setup.py install

SnapATAC2

找到安装包的位置，修改snapatac2/plotting/__init__.py中的255行

# line 255
count = pl.DataFrame(aggregate_X(data, groupby=groupby, normalize="RPKM"))
# 修改为
out_adata = aggregate_X(data, groupby=groupby, normalize="RPKM")
count = pl.DataFrame(out_adata.to_df().T)

找到安装包的位置，修改snapatac2/tools/_diff.py中的22行

# line 22
count = pl.DataFrame(aggregate_X(data, groupby=groupby, normalize="RPKM"))
# 修改为
out_adata = aggregate_X(data, groupby=groupby, normalize="RPKM")
count = pl.DataFrame(out_adata.to_df().T)

下载基因组注释文件

mkdir -p ~/DataHub/Genomics/GENCODE
cd ~/DataHub/Genomics/GENCODE
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.chr_patch_hapl_scaff.basic.annotation.gff3.gz
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/GRCh38.primary_assembly.genome.fa.gz
gunzip GRCh38.primary_assembly.genome.fa.gz

Reference

https://cloud.tencent.com/developer/article/1624514
https://kzhang.org/SnapATAC2

声明：本文内容由网友自发贡献，本站不承担相应法律责任。对本内容有异议或投诉，请联系2913721942#qq.com核实处理，我们将尽快回复您，谢谢合作！