nhoffman

---
title: [title]
author: Noah Hoffman
date: "`r format(Sys.time(), '%Y-%m-%d')`"
output:
  html_document:
    toc: true
---

# setup

nhoffman

from scipy.interpolate import interp1d
import numpy as np

import shlex
import subprocess as sp

import prettyplotlib as ppl
from matplotlib import pyplot as plt
from matplotlib.ticker import FuncFormatter
import io

nhoffman

tmux notes

sessions

Create a new session then rename it:

C-b :new
C-b $

Create a new named session:

nhoffman

import os
import sys

# Ensure that a virtualenv is active before importing non-stdlib dependencies.
venv = os.environ.get('VIRTUAL_ENV')
if not venv:
    sys.exit('--> an active virtualenv is required'.format(venv))

from SCons.Script import (Environment, Variables, Help, Decider)

nhoffman

#!/bin/bash

# Requires argparse.bash (https://github.com/nhoffman/argparse-bash)
# in the same directory as this script

# Installation:
# cd ~/bin  # or another location on your $PATH
# curl https://gist.githubusercontent.com/nhoffman/8636c6e267cb4403ac3a35ff0bc53f3d/raw/ > ssh-tunnel
# chmod +x ssh-tunnel
# curl -O https://raw.githubusercontent.com/nhoffman/argparse-bash/master/argparse.bash

nhoffman

#!/usr/bin/python2.7
"""

Performs a web BLAST query against NR using DNA sequences read from a fasta
file, storing the results in a SQLite database.

Dependencies: BioPython
    BioPython may be installed using the Python package index:
    $ sudo easy_install -f http://biopython.org/DIST/ biopython

nhoffman

#!/bin/bash

# Incremental backup using rsync
# see http://www.mikerubel.org/computers/rsync_snapshots/#Incremental

set -e

BACKUP_DIR=backup

rot_cycle_days=7  # for example

nhoffman

#!/usr/bin/env Rscript

if(Sys.getenv("VIRTUAL_ENV") == ""){ stop("An active virtualenv is required") }
source(file.path(Sys.getenv('VIRTUAL_ENV'), 'bin', 'rvenv'))

suppressPackageStartupMessages(library(argparse, quietly = TRUE))
suppressPackageStartupMessages(library(rmarkdown, quietly = TRUE))


main <- function(arguments){

nhoffman

import os
import sys
import ConfigParser
from os import path, environ
import glob
import itertools

venv = environ.get('VIRTUAL_ENV')
if not venv:
    sys.exit('--> an active virtualenv is required'.format(venv))

nhoffman

sshmount () {
	# Usage: sshmount host directory
	host=$1
	pth=$2
	mountpoint=~/mnt/${host}+$(basename $pth)
	mkdir -p $mountpoint
	sshfs $host:$pth $mountpoint -oauto_cache,reconnect,defer_permissions,negative_vncache,volname=${host}+$(basename $pth)
	cd $mountpoint
	echo "unmount using: umount $mountpoint"
}