bmmalone

#! /usr/bin/env bash

###
# This is `Zarat`'s comment to `leo`'s answer from this SO thread:
#     https://stackoverflow.com/questions/3497123
#
# Plus some additional logic to checkout a branch, if specified
###
set -x # echo on

bmmalone

#! /usr/bin/env bash

export STAR_VERSION=2.5.3a
export SAMTOOLS_VERSION=1.4.1
export BOWTIE2_VERSION=2.3.2
export SEQAN_VERSION=2.2.0
export FLEXBAR_VERSION=3.0.3
export BITSEQ_VERSION=0.7.5

sudo apt-get install libtbb-dev

bmmalone

%%%
% Add spaces when necessary after commands
%%%
\usepackage{xspace}


%%%
% Make sure we can use colors
%%%
\usepackage{xcolor}

bmmalone

\documentclass[a4paper,10pt]{article}

% make writing commands easier
\usepackage{xparse}

% colored text
\usepackage{color}

% include eps, pdf graphics
\usepackage{graphicx}

bmmalone

#! /usr/bin/env bash

sudo apt-get --assume-yes install build-essential
sudo apt-get --assume-yes install gfortran
sudo apt-get --assume-yes install zlib1g-dev
sudo apt-get --assume-yes install libreadline-dev
sudo apt-get --assume-yes install libncursesw5-dev
sudo apt-get --assume-yes install lib32ncurses5-dev
sudo apt-get --assume-yes install libgdbm-dev
sudo apt-get --assume-yes install libsqlite3-dev

bmmalone

# largely from here: https://gist.github.com/justin808/9493723

set -g mode-mouse on
set -g mouse-resize-pane on
set -g mouse-select-pane on
set -g mouse-select-window on

# Toggle mouse on
bind m \
	set -g mode-mouse on \;\

bmmalone

syntax on
set autoindent
set number

" try to handle tabs in makefiles correctly
filetype plugin on

" change to the directory of the current file by default
" workaround. see: https://github.com/vim/vim/issues/704
autocmd VimEnter * set autochdir

bmmalone

#! /usr/bin/env bash

ps aux | grep -E $USER.*$1 | grep -v 'grep\|-bash\|sshd:\|ps aux\|less' | less

bmmalone

#! /usr/bin/env python3

import argparse
import os.path
import shutil
import subprocess

user_home = os.path.expanduser('~')
default_template_file = os.path.join(
    user_home,

bmmalone

#! /usr/bin/env bash

epstool --copy --bbox $1.eps $1.bb.eps
rm $1.eps
mv $1.bb.eps $1.eps
convert $1.eps $1.png