
生信探索
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2023/04/07阅读:22主题:姹紫
使用homebrew管理linux和mac的包
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添加镜像
linux和apple都一样,先添加变量
export HOMEBREW_INSTALL_FROM_API=1
export HOMEBREW_API_DOMAIN="https://mirrors.tuna.tsinghua.edu.cn/homebrew-bottles/api"
export HOMEBREW_BOTTLE_DOMAIN="https://mirrors.tuna.tsinghua.edu.cn/homebrew-bottles"
export HOMEBREW_BREW_GIT_REMOTE="https://mirrors.tuna.tsinghua.edu.cn/git/homebrew/brew.git"
export HOMEBREW_CORE_GIT_REMOTE="https://mirrors.tuna.tsinghua.edu.cn/git/homebrew/homebrew-core.git"
export HOMEBREW_API_DOMAIN="https://mirrors.tuna.tsinghua.edu.cn/homebrew-bottles/api"
export HOMEBREW_BREW_GIT_REMOTE="https://mirrors.tuna.tsinghua.edu.cn/git/homebrew/brew.git"
Apple M2
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安装CLT for Xcode
xcode-select --install
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安装brew
git clone --depth=1 https://mirrors.tuna.tsinghua.edu.cn/git/homebrew/install.git brew-install
/bin/bash brew-install/install.sh
rm -rf brew-install
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加入环境变量
test -r ~/.bash_profile && echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> ~/.bash_profile
test -r ~/.zprofile && echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> ~/.zprofile
Ubuntu 22.4
需要git 和 curl
无root
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安装到~/homebrew
cd ~
mkdir homebrew && curl -L https://github.com/Homebrew/brew/tarball/master | tar xz --strip 1 -C homebrew
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加入环境变量
mkdir -p ~/APP/bin
export PATH=$HOME/APP/bin:$PATH
ln -s $HOME/homebrew/bin/brew $HOME/APP/bin/brew
有root
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安装
git clone --depth=1 https://mirrors.tuna.tsinghua.edu.cn/git/homebrew/install.git brew-install
/bin/bash brew-install/install.sh
rm -rf brew-install
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加入环境变量
test -d ~/.linuxbrew && eval "$(~/.linuxbrew/bin/brew shellenv)"
test -d /home/linuxbrew/.linuxbrew && eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"
test -r ~/.bash_profile && echo "eval \"\$($(brew --prefix)/bin/brew shellenv)\"" >> ~/.bash_profile
test -r ~/.profile && echo "eval \"\$($(brew --prefix)/bin/brew shellenv)\"" >> ~/.profile
test -r ~/.zprofile && echo "eval \"\$($(brew --prefix)/bin/brew shellenv)\"" >> ~/.zprofile
更新
brew update
Uninstall
-p
是homebrew的安装路径,root安装的homebrew有默认路径,不需要卸载的时候指定这个参数
cd ~
wget https://raw.githubusercontent.com/Homebrew/install/HEAD/uninstall.sh
bash uninstall.sh -p ~/homebrew
安装mamba
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linux
linux上只能安装micromamba
brew install micromamba
# 手动安装mamba
wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
bash Mambaforge-Linux-x86_64.sh
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Apple M2
brew install --cask mambaforge
# 单细胞分析环境
mamba create -n SC && mamba activate SC
mamba install -y -c conda-forge python=3.10 notebook ipywidgets pandas numpy seaborn matplotlib ipykernel openpyxl pyarrow scanpy python-igraph leidenalg pytables jaxlib leidenalg
Reference
https://mirrors.tuna.tsinghua.edu.cn/help/homebrew/
https://docs.brew.sh/Installation#alternative-installs
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