run_once_install_packages.sh.tmpl

{{ if eq .chezmoi.os "linux" -}}
#!/bin/sh

# Install example
# src: https://stackoverflow.com/questions/592620/how-can-i-check-if-a-program-exists-from-a-bash-script
#if ! [ -x "$(command -v git)" ]
#then
#  echo 'Error: git is not installed.' >&2
#  exit 1
#else
#  echo "git already installed"
#fi


# Install nvim and packages
if ! [ -x "$(command -v nvim)" ]
then
  echo 'Installing neovim'
  sudo apt-get install neovim -y
  nvim +":PlugInstall" -"qa"
else
  echo 'nvim already installed'
fi

# Install miniconda3 and them mamba

if ! [ -x "$(command -v conda)" ]
then
# src:https://github.com/phargogh/dotfiles-chezmoi/blob/main/run_once_install-packages.sh.tmpl
  echo 'Installing conda'
  MINICONDA_FILE=Miniconda3-py39_4.9.2-Linux-x86_64.sh
  wget https://repo.anaconda.com/miniconda/$MINICONDA_FILE
 # check the SHA256sum of Miniconda before executing.
  echo "536817d1b14cb1ada88900f5be51ce0a5e042bae178b5550e62f61e223deae7c $MINICONDA_FILE" | sha256sum --check || exit 1  
  bash $MINICONDA_FILE
 # init conda and add channels
  conda init
  conda config --add channels conda-forge
  conda config --add channels bioconda
 # install mamba
  conda install mamba -c conda-forge
else
  echo "conda already installed"
fi


# Install nextflow

if ! [ -x "$(command -v nextflow)" ]
then
  echo 'installing nextflow'
  curl -s https://get.nextflow.io | bash
else
  echo "nextflow already installed"
fi
#Install doom emacs:

if ! [ -x "$(command -v emacs)" ]
then
  echo 'Installing doom emacs'
  sudo add-apt-repository ppa:kelleyk/emacs
  sudo apt-get update
  sudo apt-get install emacs27 ripgrep fd-find -y

  git clone --depth 1 https://github.com/hlissner/doom-emacs ~/.emacs.d
  bash ~/.emacs.d/bin/doom install
else
  echo "doom emacs already installed"
fi
bash ~/.emacs.d/bin/doom sync

# install other softwares
# github cli
# curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | sudo dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg
# echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | sudo tee /etc/apt/sources.list.d/github-cli.list > /dev/null
# sudo apt update
# sudo apt install gh -y

# important stuff
sudo apt-get install htop neofetch sqlite pandoc csvkit powershell -y
pip3 install rich-cli
curl -sS https://starship.rs/install.sh | sh

{{ end -}}