Initial Commit

dot_condarc

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+auto_activate_base: false
+changeps1: false

dot_cows

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+default
+cower
+moofasa
+mutilated
+skeleton
+small
+supermilker
+three-eyes
+udder
+vader
+www
+bell
+birdstale
+bull
+compucow
+longhorn
+papal
+pie
+resting
+super

dot_julia/config/startup.jl

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+try
+    using OhMyREPL
+    enable_autocomplete_brackets(false)
+catch e
+    @warn "Error initalizing OhMyREPL" exception=(e, catch_backtrace())
+end
+try
+    using Revise
+catch e
+    @warn "Error initalizing Revise" exception=(e, catch_backtrace())
+end

dot_nextflow/config.tmpl

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+tower {
+  enabled = true
+  accessToken = {{ (bitwarden "item" "d41ac952-d8b5-4d20-a42a-ad8e0174d152").login.password }}
+}

dot_screenrc

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+shell /usr/bin/zsh
+startup_message off
+hardstatus alwayslastline
+hardstatus string "%{= KW} %H %{= Kw}|%{-} %-Lw%{= bW}%n%f %t%{-}%+Lw %=%C%a %Y-%M-%d"

dot_tmux.conf

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+set -g default-terminal "xterm-256color"
+source "/usr/share/tmux/powerline.conf"

executable_dot_Renviron

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+## Change library to constant location for all R 4.x versions
+R_LIBS_SITE=~/R/library

executable_dot_bashrc

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+# .bashrc
+
+# Source global definitions
+if [ -f /etc/bashrc ]; then
+    . /etc/bashrc
+fi
+
+# User specific environment
+if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]]
+then
+    PATH="$HOME/.local/bin:$HOME/bin:$PATH"
+fi
+export PATH
+
+# Uncomment the following line if you don't like systemctl's auto-paging feature:
+# export SYSTEMD_PAGER=
+
+# User specific aliases and functions
+
+# Make the prompt pretty, just in case we're stuck in bash land
+export PS1="[\[\e[32m\]\u\[\e[m\]@\[\e[33m\]\h\[\e[m\] \[\e[34m\]\W\[\e[m\]] \\$ "

executable_dot_gitconfig.tmpl

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+[user]
+	name = {{ .name }}
+	email = {{ .email }}
+	signingkey = {{ .pubkey }}
+[core]
+	editor = nano
+[credential]
+	helper = store
+[color]
+	ui = auto
+[init]
+	defaultBranch = master
+[github]
+	user = MillironX
+{{- if eq .chezmoi.osRelease.id "fedora" }}
+[diff]
+	tool = kdiff3
+[merge]
+	tool = kdiff3
+{{- end }}

executable_dot_zshrc

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+# Enable Powerlevel10k instant prompt. Should stay close to the top of ~/.zshrc.
+# Initialization code that may require console input (password prompts, [y/n]
+# confirmations, etc.) must go above this block; everything else may go below.
+if [[ -r "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh" ]]; then
+  source "${XDG_CACHE_HOME:-$HOME/.cache}/p10k-instant-prompt-${(%):-%n}.zsh"
+fi
+
+# Load the antigen library
+if [[ ! -f "$HOME/.antigen.zsh" ]]; then
+  curl -L git.io/antigen > $HOME/.antigen.zsh
+fi
+source "$HOME/.antigen.zsh"
+
+# Load the oh-my-zsh library
+antigen use oh-my-zsh
+
+# Default bundles
+antigen bundle git
+antigen bundle gitignore
+antigen bundle colored-man-pages
+antigen bundle cp
+antigen bundle screen
+antigen bundle npm
+antigen bundle bundler
+antigen bundle extract
+
+# Custom bundles
+antigen bundle zsh-users/zsh-syntax-highlighting
+antigen bundle zsh-users/zsh-autosuggestions
+antigen bundle zsh-users/zsh-completions
+antigen bundle esc/conda-zsh-completion
+antigen bundle RobSis/zsh-completion-generator
+antigen bundle kloetzl/biozsh
+antigen bundle millironx/cowsay-cows
+
+DEFAULT_USER="$USER"
+
+# Theming: if I have a nerd fond, use it to the fullest extent possible
+# If not, check for basic powerline, then fall back to text-based
+# The presence of nerd fonts and/or powerline fonts will be designated
+# by the presence of a ".nf" and ".powerline" file in the home directory,
+# respectively
+source /etc/os-release
+if [[ -f "$HOME/.nf" ]]; then
+  # Nerd font config flag set
+  antigen theme romkatv/powerlevel10k
+else
+  if [[ -f "$HOME/.powerline" ]]; then
+    # Powerline config flag set
+    antigen theme https://gist.github.com/e95df0a0aa6d1721e85b905399971515.git believer
+  else
+    # Powerline config flag not set
+    antigen theme https://gist.github.com/efde5e8d507bd3e1e046198b69d579f8.git gianu-improved
+  fi
+fi
+
+# oh-my-zsh configuration settings
+HYPHEN_INSENSITIVE="true"
+ENABLE_CORRECTION="true"
+COMPLETION_WAITING_DOTS="true"
+
+# >>> conda initialize >>>
+# !! Contents within this block are managed by 'conda init' !!
+__conda_setup="$('$HOME/miniconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
+if [ $? -eq 0 ]; then
+    eval "$__conda_setup"
+else
+    if [ -f "$HOME/miniconda3/etc/profile.d/conda.sh" ]; then
+        . "$HOME/miniconda3/etc/profile.d/conda.sh"
+    else
+        export PATH="$HOME/miniconda3/bin:$PATH"
+    fi
+fi
+unset __conda_setup
+# <<< conda initialize <<<
+
+# >>> rbenv initialize >>>
+export PATH="$HOME/.rbenv/bin:$PATH"
+eval "$(rbenv init -)"
+export PATH="$HOME/.rbenv/plugins/ruby-build/bin:$PATH"
+# <<< rbenv initialize <<<
+
+# >>> n initalize >>>
+export N_PREFIX=$HOME/.n
+export PATH="$HOME/.n/bin:$PATH"
+# <<< n initialize <<<
+
+# >>> direnv initalize >>>
+eval "$(direnv hook zsh)"
+# <<< direnv initalize <<<
+
+# >>> homebrew initalize >>>
+export fpath=(/home/linuxbrew/.linuxbrew/share/zsh/site-functions $fpath)
+eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"
+# <<< homebrew initalize <<<
+
+# Tell Antigen that you're done
+antigen apply
+
+# User configuration
+# Setup bash completion support
+# (zsh completion support is handled by oh-my-zsh)
+autoload -U bashcompinit
+bashcompinit
+
+# Add pipx packages to PATH
+export PATH="$PATH:$HOME/.local/bin"
+# Enable pipx completions
+if [[ $(command -v pipx) ]]; then
+  eval "$(register-python-argcomplete pipx)"
+fi
+
+# Preferred editor for local and remote sessions
+if [[ $(command -v nano) ]]; then
+  export EDITOR=nano
+fi
+
+# Set a cool new pager with color support
+if [[ $(command -v most) ]]; then
+  export PAGER=most
+fi
+
+# Fix screen wrapping if on a local terminal
+# (Will cause problems if set twice, i.e. in
+# both local and remote sessions)
+if [ ! -n "$SSH_CONNECTION" ]; then
+  ZLE_RPROMPT_INDENT=0
+fi
+
+# Personal aliases
+alias zshconfig="$EDITOR ~/.zshrc"
+alias ohmyzsh="$EDITOR ~/.oh-my-zsh"
+alias zshrefresh="source ~/.zshrc"
+
+# Dotfiles sync command
+alias config='/usr/bin/git --git-dir=$HOME/.cfg/ --work-tree=$HOME'
+
+# Check for Ubuntu's name for bat
+if [[ $(command -v batcat) ]]; then
+  alias bat="batcat"
+fi
+
+# Replace cat with bat
+if [[ $(command -v bat) ]]; then
+  alias cat="bat"
+  export BAT_PAGER="less -RF"
+  export MANPAGER="sh -c 'col -bx | bat -l man -p'"
+  export MANROFFOPT="-c"
+fi
+
+# Replace ls with lsd
+if [[ $(command -v lsd) ]]; then
+  alias ls="lsd"
+fi
+
+# Add notification support for long-running processes
+if [[ $(command -v ntfy) ]]; then
+  eval "$(ntfy shell-integration --longer-than 30)"
+  export AUTO_NTFY_DONE_IGNORE="vim nano emacs zshconfig screen tmux ssh top htop less more most nethogs 'singularity shell' julia man"
+fi
+
+# Replace VSCode with pure FOSS alternative
+if [[ $(command -v codium) ]] && [[ ! $(command -v code) ]]; then
+  alias code="codium"
+fi
+
+# Make forgetting sudo less painful
+alias please='sudo $(fc -ln -1)'
+
+# Make and change directories in one easy step
+# nd = New Directory
+nd () {
+  mkdir "$1"
+  cd "$1"
+}
+
+# Make running programs on the GPU less painful
+alias nrun='__NV_PRIME_RENDER_OFFLOAD=1 __GLX_VENDOR_LIBRARY_NAME=nvidia __VK_LAYER_NV_optimus="NVIDIA_only"'
+
+# Set the Nextflow enviroment caches
+export NXF_HOME="$HOME/.nextflow"
+export NXF_CONDA_CACHEDIR="$NXF_HOME/conda"
+export NXF_SINGULARITY_CACHEDIR="$NXF_HOME/singularity"
+export NXF_CHARLIECLOUD_CACHEDIR="$NXF_HOME/charlie"
+
+# To customize prompt, run `p10k configure` or edit ~/.p10k.zsh.
+[[ ! -f ~/.p10k.zsh ]] || source ~/.p10k.zsh

private_dot_gnupg/private_gpg-agent.conf

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+default-cache-ttl 10000
+max-cache-ttl 86400