bdunnette

#!/bin/sh
# To get an Ubuntu 16.04 XFCE desktop: sudo sh -e ~/Downloads/crouton -t xfce,cli-extra,xiwi,extension -r xenial
# For CLI-only: sudo sh -e ~/Downloads/crouton -t cli-extra -r xenial
# To run the latest version: 
# curl https://gist.githubusercontent.com/bdunnette/75fdc4b15b9599cd5fdf/raw/setup-chroot.sh | sh
sudo apt-get install -y nano curl git language-pack-en build-essential software-properties-common 
sudo echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
sudo apt-get update

bdunnette

ssh user1234@my-virtual-host.oit.umn.edu
sudo su - swadm
sudo su - mysql
mysql -u root -p
CREATE USER 'olab'@'localhost' IDENTIFIED BY 'my_olab_database_password';
GRANT ALL PRIVILEGES ON olab.* TO 'olab'@'localhost';
OAuth callback URL: http://my-virtual-host.oit.umn.edu/home/loginOAuthCallback

bdunnette

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
A constant-space parser for the GeneOntology OBO v1.2 format

Modified from work by Uli Koehler: http://techoverflow.net/blog/2013/11/18/a-geneontology-obo-v1.2-parser-in-python/
"""
from __future__ import with_statement
from collections import defaultdict
import types

bdunnette

#!/bin/bash
for s in *.svs
do
  echo "$s"
  #To generate a reasonable-sized JPEG, we'll export level 1 of the SVS file (level 0 = full magnification, which many image processing programs don't handle well)
  time vips jpegsave $s[level=1] $s.jpeg
done

bdunnette

import sys
import gspread
import requests

cases = requests.get("http://slides.pathology.umn.edu/ISP/cases.json").json()

# Login with your Google account
gc = gspread.login(sys.argv[1], sys.argv[2])

# Open a worksheet from spreadsheet with one shot

bdunnette

function sendEmails() {
  var sheet = SpreadsheetApp.getActiveSheet();
  var startRow = 2;  // First row of data to process
  var dataRange = sheet.getRange(startRow, 1, sheet.getLastRow(), sheet.getLastColumn())
  // Fetch values for each row in the Range.
  var data = dataRange.getValues();
  for (i in data) {
    var row = data[i];
    var notificationSent = row[3];
    Logger.log(notificationSent);

bdunnette

#!/bin/sh

echo "Extracting HTML Files"

for f in ~/*.tar
do
  tar xvf "$f" --wildcards '*.html'
done

for n in 0 1 2 3 4 5 6 7 8 9

bdunnette

import feedparser
import urllib

feed = feedparser.parse('http://ws.audioscrobbler.com/2.0/user/lazymofo/podcast.rss')

for item in feed.entries:
    item_url = item.links[0].href
    print item_url
    file = urllib.urlretrieve(item_url)

bdunnette

#!/usr/bin/env python
import hashlib
import os
import sys
import csv
 
# Set the directory you want to start from
rootDir = sys.argv[1]
BLOCKSIZE = 65536
csv_filename = "checksums.csv"

bdunnette

import sys
import os
import os.path
import zipfile
from lxml import etree
from lxml import objectify

tempdir = 'temp'
docfile = zipfile.ZipFile(sys.argv[1])
docfile.extractall(tempdir)