Merge branch 'master' of https://git.charlesreid1.com/dotfiles/rivanna

* 'master' of https://git.charlesreid1.com/dotfiles/rivanna:
  skip bootstrap.sh in bootstrap.sh
  fix rivanna dotfiles

.aliases

@@ -0,0 +1,136 @@
+#!/usr/bin/env bash
+
+
+# lazy af
+alias mk='make'
+alias smk='snakemake'
+alias smake='snakemake'
+alias py='python3'
+alias ipy='ipython --pylab'
+alias ip="dig +short myip.opendns.com @resolver1.opendns.com"
+alias ipaddr="dig +short myip.opendns.com @resolver1.opendns.com"
+
+
+# one-letter aliases
+# ---------------
+alias h='echo ""; echo $HOSTNAME; echo ""'
+alias p='echo -e ${PATH//:/\\n}'
+alias e='exit'
+alias u='cd ..'
+alias v='vim'
+
+
+
+# utility wrappers
+# ---------------
+alias pp='python setup.py build && python setup.py install'
+alias sha1='openssl sha1'
+alias du='du -kh'
+alias dh='dh -kTh'
+alias pc='pelican content'
+
+
+
+
+# don't clobber
+# -----------------
+alias rm='rm -i'
+alias cp='cp -i'
+alias mv='mv -i'
+
+
+
+
+
+# ls aliases
+# -------------------- 
+# Detect which `ls` flavor is in use
+if ls --color > /dev/null 2>&1; then # GNU `ls`
+    colorflag="--color"
+    export LS_COLORS='no=00:fi=00:di=01;31:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.avi=01;35:*.fli=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.ogg=01;35:*.mp3=01;35:*.wav=01;35:'
+    groupflag="--group-directories-first"
+else # macOS `ls`
+    colorflag="-G"
+    export LSCOLORS='BxBxhxDxfxhxhxhxhxcxcx'
+    groupflag=""
+fi
+
+
+
+alias ls="/bin/ls -1 ${colorflag} ${groupflag}"
+alias sl='ls'
+
+
+
+# List all files colorized in long format
+alias l="/bin/ls -lhAF ${colorflag}"
+alias ll="l"
+
+# List all files colorized in long format, including dot files
+alias la="l -a"
+
+# List only directories
+alias lsd="/bin/ls -lF ${colorflag} | grep --color=never '^d'"
+
+
+alias lr='ls -r' # reverse
+alias llr='ll -r' # reverse
+
+alias lt='/bin/ls -lhAFt -G' # time
+
+alias lt='ls -t' # time
+alias llt='ll -t' # time
+
+alias ltr='ls -tr' # reverse time
+alias lltr='ll -tr' # reverse time
+
+alias lk='ls -lSr' # by size (small to big)
+
+
+
+
+# clear 
+# ---------------
+alias clc='clear; pwd'
+alias cl='clc; ll'
+alias cll='clear; ll'
+alias cls='clear; ls'
+alias lcs='clear; ls'
+alias csl='cls'
+alias cla='clear; la'
+alias c='clear'
+
+
+
+
+
+# typo aliases
+# ---------------
+alias lll='ll'
+alias mdkir='mkdir'
+alias mdir='mkdir'
+alias celar='clear'
+alias cealr='clear'
+
+
+
+# cd 
+# ---------------
+alias back='cd $OLDPWD'
+
+
+
+
+
+####################
+# modified mathias
+
+# Always enable colored `grep` output
+# Note: `GREP_OPTIONS="--color=auto"` is deprecated, hence the alias usage.
+alias grep='grep --color=auto'
+
+# Get week number
+alias week='date +%V'
+
+# Print each PATH entry on a separate line
+alias path='echo -e ${PATH//:/\\n}'

.bash_profile

@@ -0,0 +1,75 @@
+# This is the bash profile.
+# 
+# This file sets PATH and bash options.
+#
+# to add your own non-committed machine-specific settings,
+# use ~/.extras
+
+# Must
+EDITOR="vim"
+GIT_EDITOR="vim"
+
+
+
+
+# Python:
+# Try not to have to deal with PYTHONPATH...
+
+# Go
+#export PATH="${HOME}/.local/bin:${PATH}"
+
+# Pyenv
+export PATH="${HOME}/.pyenv/bin:${PATH}"
+
+#
+# This ALWAYS complains when starting up the node.
+# Don't add this to .bash_profile until the pyenv script is finished.
+# 
+# only include this if you want to activate your env by default.
+# you should also install a pyenv version!
+eval "$(pyenv init -)"
+#eval "$(pyenv virtualenv-init -)"
+
+
+# Bash history
+
+HISTFILE="$HOME/.bash_history"
+HISTFILESIZE=1000000000
+HISTIGNORE="ls:cls:clc:clear:pwd:l:ll:[ ]*"
+HISTSIZE=1000000
+HISTTIMEFORMAT=': %Y-%m-%d_%H:%M:%S; '
+
+# Append to the Bash history file, rather than overwriting it
+shopt -s histappend;
+# Save Bash history 
+shopt -s cmdhist;
+
+
+
+
+#############################
+# modified mathias
+
+# Load the shell dotfiles, and then some:
+# * ~/.path can be used to extend `$PATH`.
+# * ~/.extras can be used for other settings you don’t want to commit.
+for file in ~/.{path,bash_prompt,exports,aliases,functions,extras}; do
+	[ -r "$file" ] && [ -f "$file" ] && source "$file";
+done;
+unset file;
+
+# Case-insensitive globbing (used in pathname expansion)
+shopt -s nocaseglob;
+
+# Autocorrect typos in path names when using `cd`
+shopt -s cdspell;
+
+
+# Enable tab completion for `g` by marking it as an alias for `git`
+if type _git &> /dev/null && [ -f /usr/local/etc/bash_completion.d/git-completion.bash ]; then
+	complete -o default -o nospace -F _git g;
+fi;
+
+# Add tab completion for SSH hostnames based on ~/.ssh/config, ignoring wildcards
+[ -e "$HOME/.ssh/config" ] && complete -o "default" -o "nospace" -W "$(grep "^Host" ~/.ssh/config | grep -v "[?*]" | cut -d " " -f2- | tr ' ' '\n')" scp sftp ssh;
+

.bash_prompt

@@ -0,0 +1,74 @@
+#!/usr/bin/env bash
+
+# Shell prompt based on the Solarized Dark theme.
+# Screenshot: http://i.imgur.com/EkEtphC.png
+# Heavily inspired by @necolas’s prompt: https://github.com/necolas/dotfiles
+# iTerm → Profiles → Text → use 13pt Monaco with 1.1 vertical spacing.
+
+if [[ $COLORTERM = gnome-* && $TERM = xterm ]] && infocmp gnome-256color >/dev/null 2>&1; then
+	export TERM='gnome-256color';
+elif infocmp xterm-256color >/dev/null 2>&1; then
+	export TERM='xterm-256color';
+fi;
+
+if tput setaf 1 &> /dev/null; then
+	tput sgr0; # reset colors
+	bold=$(tput bold);
+	reset=$(tput sgr0);
+	# Solarized colors, taken from http://git.io/solarized-colors.
+	black=$(tput setaf 0);
+	blue=$(tput setaf 33);
+	cyan=$(tput setaf 37);
+	green=$(tput setaf 64);
+	orange=$(tput setaf 166);
+	purple=$(tput setaf 125);
+	red=$(tput setaf 124);
+	violet=$(tput setaf 61);
+	white=$(tput setaf 15);
+	yellow=$(tput setaf 136);
+else
+	bold='';
+	reset="\e[0m";
+	black="\e[1;30m";
+	red="\e[1;31m";
+	green="\e[1;32m";
+	orange="\e[1;33m";
+	yellow="\e[1;33m";
+	blue="\e[1;34m";
+	purple="\e[1;35m";
+	violet="\e[1;35m";
+	cyan="\e[1;36m";
+	white="\e[1;37m";
+fi;
+
+# Ravenna is cyan
+userStyle="${cyan}"
+
+# Highlight the hostname when connected via SSH.
+if [[ "${SSH_TTY}" ]]; then
+	hostStyle="${bold}${userStyle}";
+else
+	hostStyle="${userStyle}";
+fi;
+
+# Root username is red
+if [[ "${USER}" == "root" ]]; then
+	userStyle="${red}";
+fi;
+
+# Set the terminal title and prompt.
+PS1="\[\033]0;\W\007\]"; # working directory base name
+PS1+="\[${bold}\]\n"; # newline
+PS1+="\[${userStyle}\]\u"; # username
+PS1+="\[${white}\] on ";
+PS1+="\[${hostStyle}\]\h"; # host
+PS1+="\[${white}\] at ";
+PS1+="[ \D{%Y-%m-%d} - \t ] in "; # date and time stamp
+#PS1+="\[${green}\]\w"; # working directory full path
+PS1+="\w"; # working directory full path
+PS1+="\n";
+PS1+="\[${white}\]\$ \[${reset}\]"; # `$` (and reset color)
+export PS1;
+
+PS2="\[${yellow}\]→ \[${reset}\]";
+export PS2;

.gitconfig

@@ -0,0 +1,189 @@
+[user]
+    email = charlesreid1@gmail.com
+    name = Charles Reid
+[credential]
+    helper = cache
+[filter "media"]
+    clean = git-media-clean %f
+    smudge = git-media-smudge %f
+[push]
+    default = simple
+[alias]
+
+    # courtesy of https://stackoverflow.com/a/34467298
+    lg = !"git lg1"
+    lg1 = !"git lg1-specific --all"
+    lg2 = !"git lg2-specific --all"
+    lg3 = !"git lg3-specific --all"
+
+    lg1-specific = log --graph --abbrev-commit --decorate --format=format:'%C(bold blue)%h%C(reset) - %C(bold green)(%ar)%C(reset) %C(white)%s%C(reset) %C(dim white)- %an%C(reset)%C(auto)%d%C(reset)'
+    lg2-specific = log --graph --abbrev-commit --decorate --format=format:'%C(bold blue)%h%C(reset) - %C(bold cyan)%aD%C(reset) %C(bold green)(%ar)%C(reset)%C(auto)%d%C(reset)%n''          %C(white)%s%C(reset) %C(dim white)- %an%C(reset)'
+    lg3-specific = log --graph --abbrev-commit --decorate --format=format:'%C(bold blue)%h%C(reset) - %C(bold cyan)%aD%C(reset) %C(bold green)(%ar)%C(reset) %C(bold cyan)(committed: %cD)%C(reset) %C(auto)%d%C(reset)%n''          %C(white)%s%C(reset)%n''          %C(dim white)- %an <%ae> %C(reset) %C(dim white)(committer: %cn <%ce>)%C(reset)'
+
+
+    # View abbreviated SHA, description, and history graph of the latest 20 commits
+    l = log --pretty=oneline -n 20 --graph --abbrev-commit
+
+    # View the current working tree status using the short format
+    s = status -s
+
+    b = branch -v
+    bv = branch -v
+    ba = branch -a
+
+    r = remote -v
+    rv = remote -v
+
+    cdiff = diff --cached
+
+    # Show the diff between the latest commit and the current state
+    d = !"git diff-index --quiet HEAD -- || clear; git --no-pager diff --patch-with-stat"
+
+    # `git di $number` shows the diff between the state `$number` revisions ago and the current state
+    di = !"d() { git diff --patch-with-stat HEAD~$1; }; git diff-index --quiet HEAD -- || clear; d"
+
+    # Pull in remote changes for the current repository and all its submodules
+    p = !"git pull; git submodule foreach git pull origin master"
+
+    # Clone a repository including all submodules
+    c = clone --recursive
+
+    # Commit all changes
+    ca = !git add -A && git commit -av
+
+    # Switch to a branch, creating it if necessary
+    go = "!f() { git checkout -b \"$1\" 2> /dev/null || git checkout \"$1\"; }; f"
+
+    # Show verbose output about tags, branches or remotes
+    tags = tag -l
+    branches = branch -a
+    remotes = remote -v
+
+    # List aliases
+    aliases = config --get-regexp alias
+
+    # Amend the currently staged files to the latest commit
+    amend = commit --amend --reuse-message=HEAD
+
+    # Credit an author on the latest commit
+    credit = "!f() { git commit --amend --author \"$1 <$2>\" -C HEAD; }; f"
+
+    # Interactive rebase with the given number of latest commits
+    reb = "!r() { git rebase -i HEAD~$1; }; r"
+
+    # Remove the old tag with this name and tag the latest commit with it.
+    retag = "!r() { git tag -d $1 && git push origin :refs/tags/$1 && git tag $1; }; r"
+
+    # Find branches containing commit
+    fb = "!f() { git branch -a --contains $1; }; f"
+
+    # Find tags containing commit
+    ft = "!f() { git describe --always --contains $1; }; f"
+
+    # Find commits by source code
+    fc = "!f() { git log --pretty=format:'%C(yellow)%h  %Cblue%ad  %Creset%s%Cgreen  [%cn] %Cred%d' --decorate --date=short -S$1; }; f"
+
+    # Find commits by commit message
+    fm = "!f() { git log --pretty=format:'%C(yellow)%h  %Cblue%ad  %Creset%s%Cgreen  [%cn] %Cred%d' --decorate --date=short --grep=$1; }; f"
+
+    # List contributors with number of commits
+    contributors = shortlog --summary --numbered
+
+[apply]
+
+    # Detect whitespace errors when applying a patch
+    whitespace = fix
+
+[core]
+
+    # Use custom `.gitignore` and `.gitattributes`
+    excludesfile = ~/.gitignore
+    attributesfile = ~/.gitattributes
+
+    # Treat spaces before tabs and all kinds of trailing whitespace as an error
+    # [default] trailing-space: looks for spaces at the end of a line
+    # [default] space-before-tab: looks for spaces before tabs at the beginning of a line
+    whitespace = space-before-tab,-indent-with-non-tab,trailing-space
+
+    # Make `git rebase` safer on macOS
+    # More info: <http://www.git-tower.com/blog/make-git-rebase-safe-on-osx/>
+    ###trustctime = false
+
+    # Prevent showing files whose names contain non-ASCII symbols as unversioned.
+    # http://michael-kuehnel.de/git/2014/11/21/git-mac-osx-and-german-umlaute.html
+    precomposeunicode = false
+
+    # Speed up commands involving untracked files such as `git status`.
+    # https://git-scm.com/docs/git-update-index#_untracked_cache
+    untrackedCache = true
+
+[color]
+
+    # Use colors in Git commands that are capable of colored output when
+    # outputting to the terminal. (This is the default setting in Git ≥ 1.8.4.)
+    ui = auto
+
+[color "branch"]
+
+    current = yellow reverse
+    local = yellow
+    remote = green
+
+[color "diff"]
+
+    meta = yellow bold
+    frag = magenta bold # line info
+    old = red # deletions
+    new = green # additions
+
+[color "status"]
+
+    added = yellow
+    changed = green
+    untracked = cyan
+
+[diff]
+
+    # Detect copies as well as renames
+    renames = copies
+
+[diff "bin"]
+
+    # Use `hexdump` to diff binary files
+    textconv = hexdump -v -C
+
+[merge]
+
+    # Include summaries of merged commits in newly created merge commit messages
+    log = true
+
+[push]
+
+    # Use the Git 1.x.x default to avoid errors on machines with old Git
+    # installations. To use `simple` instead, add this to your `~/.extra` file:
+    # `git config --global push.default simple`. See http://git.io/mMah-w.
+    default = matching
+    # Make `git push` push relevant annotated tags when pushing branches out.
+    followTags = true
+
+# URL shorthands
+
+[url "git@github.com:"]
+
+    insteadOf = "gh:"
+    pushInsteadOf = "github:"
+    pushInsteadOf = "git://github.com/"
+
+[url "git://github.com/"]
+
+    insteadOf = "github:"
+
+[url "git@gist.github.com:"]
+
+    insteadOf = "gst:"
+    pushInsteadOf = "gist:"
+    pushInsteadOf = "git://gist.github.com/"
+
+[url "git://gist.github.com/"]
+
+    insteadOf = "gist:"

.gitignore

@@ -0,0 +1,2 @@
+# This file is inteded to hold machine-specific, non-git-commited info
+.extra

.hushlogin

@@ -0,0 +1,4 @@
+# The mere presence of this file in the home directory disables the system
+# copyright notice, the date and time of the last login, the message of the
+# day as well as other information that may otherwise appear on login.
+# See `man login`.

.inputrc

@@ -0,0 +1,63 @@
+#########################
+# modified mathias
+
+# Make Tab autocomplete regardless of filename case
+set completion-ignore-case on
+
+# List all matches in case multiple possible completions are possible
+set show-all-if-ambiguous on
+
+
+# from http://dotfiles.org/~brendano/.inputrc
+set blink-matching-paren on
+
+
+# Use the text that has already been typed as the prefix for searching through
+# commands (i.e. more intelligent Up/Down behavior)
+"\e[A": history-search-backward
+"\e[B": history-search-forward
+"\eOA": history-search-backward
+"\eOB": history-search-forward
+
+# control + P and control + N - go forward/back thru history
+"\C-p": history-search-backward
+"\C-n": history-search-forward
+
+"\M-p":	history-search-backward
+"\M-n":	history-search-forward
+"\M-?":	dump-functions
+
+
+## Change the mode of everything that uses readline
+#set editing-mode vi
+
+
+# Immediately add a trailing slash when autocompleting symlinks to directories
+set mark-symlinked-directories on
+
+# Do not autocomplete hidden files unless the pattern explicitly begins with a dot
+set match-hidden-files off
+
+# Show all autocomplete results at once
+set page-completions off
+
+# If there are more than 200 possible completions for a word, ask to show them all
+set completion-query-items 200
+
+# Show extra file information when completing, like `ls -F` does
+set visible-stats on
+
+# Be more intelligent when autocompleting by also looking at the text after
+# the cursor. For example, when the current line is "cd ~/src/mozil", and
+# the cursor is on the "z", pressing Tab will not autocomplete it to "cd
+# ~/src/mozillail", but to "cd ~/src/mozilla". (This is supported by the
+# Readline used by Bash 4.)
+set skip-completed-text on
+
+# Allow UTF-8 input and output, instead of showing stuff like $'\0123\0456'
+set input-meta on
+set output-meta on
+set convert-meta off
+
+# Use Alt/Meta + Delete to delete the preceding word
+"\e[3;3~": kill-word

.vimrc

@@ -0,0 +1,256 @@
+" ==============================================
+"               vanilla vimrc
+" ==============================================
+set nocompatible              " iMproved
+filetype off                  " required
+filetype plugin indent on
+"setlocal spell spelllang=en_us
+set nofoldenable    " disable folding
+
+
+
+
+" Turn off Esc+O key sequences (eliminates one-second delay when pressing O):
+" https://superuser.com/questions/161178/why-does-vim-delay-for-a-second-whenever-i-use-the-o-command-open-a-new-line#161216
+" if this is re-enabled i may stab someone.
+set noesckeys
+set ttimeoutlen=5
+
+" you have to do this a second time
+set nocompatible
+" don't break words with wrap on
+set linebreak
+" don't make these keys do annoying things
+nnoremap <F1> <nop>
+nnoremap J mzJ`z
+nnoremap n nzz
+nnoremap } }zz
+nnoremap <F1> <nop>
+nnoremap Q <nop>
+nnoremap K <nop>
+" use j and k to move among display lines, not just file lines
+noremap j gj
+noremap k gk
+" if compiled with autocmd, jump to last cursor position
+if has("autocmd")
+  " When editing a file, always jump to the last known cursor position.
+  " Don't do it when the position is invalid or when inside an event handler
+  " (happens when dropping a file on gvim).
+  autocmd BufReadPost *
+    \ if line("'\"") > 0 && line("'\"") <= line("$") |
+    \   exe "normal g`\"" |
+    \ endif
+endif " has("autocmd")
+" in Python, don't move comment hashtag to first column.
+" smartindent unnecessary for python anyway.
+" http://stackoverflow.com/questions/2063175/vim-insert-mode-comments-go-to-start-of-line
+au! FileType python setl nosmartindent
+" allow visual mode to go to blank space at end of lines
+set virtualedit=block
+" horizontal and vertical splits should go in right place
+set splitbelow
+set splitright
+" turn on syntax highlighting
+syntax on
+set ic
+" this highlights search items
+set hls
+" this highlights search items as they are typed
+set incsearch
+hi IncSearch cterm=none ctermfg=blue ctermbg=green
+" make searches case-insensitive, unless they contain upper-case letters:
+set ignorecase
+set smartcase
+" toggle search highlighting:
+" space after search turns off highlights and clears messages
+:nnoremap <silent> <Space> :nohlsearch<Bar>:echo<CR>
+" turn off splash message
+set shortmess+=I
+" allow backspacing after first insert spot
+set backspace=indent,eol,start
+" murder that cursed blinking cursor
+let &guicursor = &guicursor . ",a:blinkon0"
+" Makefiles
+au BufRead,BufNewFile Makefile*,*.make,*.mk set noexpandtab
+" C++
+au BufRead,BufNewFile *.cpp,*.cxx,*.cc,*.c,*.h,*.hpp,*.hxx,*.hh set tabstop=4 shiftwidth=4 softtabstop=4 nowrap
+" Snakemake files: Snakefile, .rule, .settings, .snake, .smk
+au BufNewFile,BufRead Snakefile set syntax=snakemake
+au BufNewFile,BufRead *.rule set syntax=snakemake
+au BufNewFile,BufRead *.settings set syntax=snakemake
+au BufNewFile,BufRead *.snake set syntax=snakemake
+au BufNewFile,BufRead *.smk set syntax=snakemake
+" Yaml
+autocmd FileType yaml setlocal ts=2 sts=2 sw=2 expandtab
+" line numbering - make it more readable
+set ruler
+" eliminate line wrapping
+set nowrap
+" tabs are 4 spaces: the *correct* way
+set tabstop=4 shiftwidth=4 expandtab
+set nosmartindent   " die die die
+" color scheme stuff
+colorscheme desert
+"colorscheme solarized
+" correct my common typos without me even noticing them:
+abbreviate teh the
+abbreviate hte the
+abbreviate reccommend recommend
+abbreviate reccomend recommend
+abbreviate recomend recommend
+abbreviate slef self
+abbreviate paramters parameters
+abbreviate exmaple example
+"
+" :e <tab> brings up longest; <tab> again shows list
+set wildmode=longest,list
+if exists('+autochdir')
+  " so :e is relative to current file
+  set autochdir
+endif
+" Running command :CD will change to current file's directory
+com! CD cd %:p:h
+" allow quit via double keypress
+map XX :q!<CR>
+map QQ :wq<CR>
+map WQ :wq<CR>
+map WW :w<CR>
+if has("user_commands")
+    command! -bang -nargs=? -complete=file E e<bang> <args>
+    command! -bang -nargs=? -complete=file W w<bang> <args>
+    command! -bang -nargs=? -complete=file Wq wq<bang> <args>
+    command! -bang -nargs=? -complete=file WQ wq<bang> <args>
+    command! -bang Wa wa<bang>
+    command! -bang WA wa<bang>
+    command! -bang Q q<bang>
+    command! -bang QA qa<bang>
+    command! -bang Qa qa<bang>
+endif
+" don't autoindent markdown files
+filetype plugin indent on
+au filetype mkd call DisableIndent()
+function! DisableIndent()
+        set autoindent&
+        set cindent&
+        set smartindent&
+        set indentexpr&
+endfunction
+" Persistent Undo
+if has("persistent_undo")
+    set undodir=~/.vim/undodir
+    set undofile
+endif
+" Shift+Tab should de-indent
+" Control + D is de-indent
+inoremap <S-Tab> <C-d>
+set autoindent
+set backspace=2                                              " Fix broken backspace in some setups
+set clipboard=unnamed                                        " yank and paste with the system clipboard
+set encoding=utf-8
+set ruler                                                    " show where you are
+set showcmd
+set smartcase                                                " case-sensitive search if any caps
+set wildignore=log/**,node_modules/**,target/**,tmp/**,*.pyc
+" keyboard shortcuts
+let mapleader = ','
+noremap <C-h> <C-w>h
+noremap <C-j> <C-w>j
+noremap <C-k> <C-w>k
+noremap <C-l> <C-w>l
+" in case you forgot to sudo
+cnoremap w!! %!sudo tee > /dev/null %
+" automatically rebalance windows on vim resize
+autocmd VimResized * :wincmd =
+" Fix Cursor in TMUX
+if exists('$TMUX')
+  let &t_SI = "\<Esc>Ptmux;\<Esc>\<Esc>]50;CursorShape=1\x7\<Esc>\\"
+  let &t_EI = "\<Esc>Ptmux;\<Esc>\<Esc>]50;CursorShape=0\x7\<Esc>\\"
+else
+  let &t_SI = "\<Esc>]50;CursorShape=1\x7"
+  let &t_EI = "\<Esc>]50;CursorShape=0\x7"
+endif
+" Don't copy the contents of an overwritten selection.
+vnoremap p "_dP
+" Enhance command-line completion
+set wildmenu
+" Allow backspace in insert mode
+set backspace=indent,eol,start
+" Optimize for fast terminal connections
+set ttyfast
+" Don’t add empty newlines at the end of files
+set noeol
+" Centralize backups, swapfiles and undo history
+set backupdir=~/.vim/backups
+set directory=~/.vim/swap
+if exists("&undodir")
+	set undodir=~/.vim/undo
+endif
+" Don’t create backups when editing files in certain directories
+set backupskip=/tmp/*,/private/tmp/*
+" Respect modeline in files
+set modeline
+set modelines=4
+" Enable per-directory .vimrc files and disable unsafe commands in them
+"""set exrc
+"""set secure
+" Enable line numbers
+set number
+" Enable syntax highlighting
+syntax on
+" Highlight current line
+set cursorline
+" Highlight searches
+set hlsearch
+" Ignore case of searches
+set ignorecase
+" Highlight dynamically as pattern is typed
+set incsearch
+" Always show status line
+set laststatus=2
+" Enable mouse in all modes
+set mouse=a
+" Disable error bells
+set noerrorbells
+" Don’t reset cursor to start of line when moving around.
+set nostartofline
+" Show the cursor position
+set ruler
+" Don’t show the intro message when starting Vim
+set shortmess+=atI
+" Show the current mode
+set showmode
+" Show the filename in the window titlebar
+set title
+" Show the (partial) command as it’s being typed
+set showcmd
+" Use relative line numbers
+if exists("&relativenumber")
+	set relativenumber
+	au BufReadPost * set relativenumber
+endif
+" Start scrolling three lines before the horizontal window border
+set scrolloff=7
+" Strip trailing whitespace (,ss)
+function! StripWhitespace()
+	let save_cursor = getpos(".")
+	let old_query = getreg('/')
+	:%s/\s\+$//e
+	call setpos('.', save_cursor)
+	call setreg('/', old_query)
+endfunction
+noremap <leader>ss :call StripWhitespace()<CR>
+" Save a file as root (,W)
+noremap <leader>W :w !sudo tee % > /dev/null<CR>
+" Automatic commands
+if has("autocmd")
+    " Enable file type detection
+    filetype on
+    " Treat .json files as .js
+    autocmd BufNewFile,BufRead *.json setfiletype json syntax=javascript
+    " Treat .md files as Markdown
+    autocmd BufNewFile,BufRead *.md setlocal filetype=markdown
+endif
+" Mark special characters
+set listchars=nbsp:☠,tab:▸␣
+"set listchars=tab:▸␣
+set list

bootstrap.sh

@@ -10,6 +10,7 @@ git pull origin master;
 function doIt() {
 	rsync \
 		--exclude ".git/" \
+		--exclude "bootstrap.sh" \
 		--exclude "cloud_init" \
 		--exclude "img" \
 		--exclude "tasks_sudo" \

queue.md

@@ -0,0 +1,55 @@
+# Rivanna queue system
+
+https://arcs.virginia.edu/slurm
+
+rivanna uses slurm for job management.
+jobs are submitted using job scripts.
+
+```
+#!/bin/bash
+#
+#SBATCH --time=12:00:00
+#SBATCH -A myaccount
+
+module load gcc/7.1.0
+./mycode
+```
+
+Other options:
+
+* `-N` number of nodes
+* `-n` number of tasks
+* `--mem` memory per task
+* `-p` partition
+* `-A` account
+
+Exporting variables:
+
+* with current value:
+
+```
+#SBATCH --export=var1, var2, var3
+```
+
+* with specific value:
+
+```
+#SBATCH --export=variable1=value1,variable2=value2
+```
+
+Stdout and Stderr:
+
+* To redirect stdout:
+
+```
+#SBATCH -o <outfile> or --output=<outfile>
+```
+
+* To redirect stderr:
+
+```
+#SBATCH -e <errfile> or --error=<errfile>
+```
+
+
+