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Brian Dunnette bdunnette

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@bdunnette
bdunnette / untar-wsi.sh
Last active August 29, 2015 14:00
Untar WSI images in zoom level order
#!/bin/sh
echo "Extracting HTML Files"
for f in ~/*.tar
do
tar xvf "$f" --wildcards '*.html'
done
for n in 0 1 2 3 4 5 6 7 8 9
@bdunnette
bdunnette / SpreadsheetNotification.js
Last active August 29, 2015 14:01
function sendEmails() {
var sheet = SpreadsheetApp.getActiveSheet();
var startRow = 2; // First row of data to process
var dataRange = sheet.getRange(startRow, 1, sheet.getLastRow(), sheet.getLastColumn())
// Fetch values for each row in the Range.
var data = dataRange.getValues();
for (i in data) {
var row = data[i];
var notificationSent = row[3];
Logger.log(notificationSent);
@bdunnette
bdunnette / json-to-gsheet.py
Created May 15, 2014 13:51
import sys
import gspread
import requests
cases = requests.get("http://slides.pathology.umn.edu/ISP/cases.json").json()
# Login with your Google account
gc = gspread.login(sys.argv[1], sys.argv[2])
# Open a worksheet from spreadsheet with one shot
@bdunnette
bdunnette / svs2jpg.sh
Created June 4, 2014 16:30
#!/bin/bash
for s in *.svs
do
echo "$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
bdunnette / obo-parser.py
Last active August 29, 2015 14:03
#!/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
bdunnette / gist:b33b5ef26a9cbdc25c98
Last active August 29, 2015 14:03
ssh [email protected]
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
bdunnette / setup-chroot.sh
Last active June 24, 2017 02:03
#!/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
bdunnette / webrtc.html
Last active August 29, 2015 14:06
<!DOCTYPE html>
<html>
<head>
<script src="http://simplewebrtc.com/latest.js"></script>
</head>
<body>
<video height="300" id="localVideo"></video>
<div id="remotesVideos"></div>
<script>
var webrtc = new SimpleWebRTC({
@bdunnette
bdunnette / meteor-skeleton.sh
Last active August 29, 2015 14:06
#!/bin/sh
mkdir -p client/compatibility client/styles client/lib client/views client/views/common lib server/lib public/images public/fonts .meteor
echo "local" > .meteor/gitignore
echo "meteor-platform\nautopublish\ninsecure\naccounts-base" > .meteor/packages
echo "[email protected]" > .meteor/release
echo "Router.configure({layoutTemplate: 'layout'}); Router.map(function() {this.route('home', {path: '/', template: 'home'});});" > client/routes.js
echo "<head><title>My App</title><meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\"><meta http-equiv=\"X-UA-Compatible\" content=\"IE=edge\"></head><body></body><template name=\"layout\">{{>navbar}}<div class=\"container-fluid\">{{>yield}} </div></template>" > client/views/common/layout.html
echo "<template name=\"navbar\"><nav class=\"navbar navbar-default\" role=\"navigation\"><div class=\"container-fluid\"><div class=\"navbar-header\"><button type=\"button\" class=\"navbar-toggle\" data-toggle=\"collapse\" data-target=\"\#bs-example-navbar-
@bdunnette
bdunnette / remindToFloss.js
Created October 8, 2014 20:36
function remindToFloss() {
var ss = SpreadsheetApp.openById("INSERT SHEET ID HERE");
var responses = ss.getSheets()[0].getDataRange();
var participants = ss.getSheets()[1].getDataRange();
var needsNotifying = [];
// Compile a list of email addresses that may need notifications
for (var i = 0; i <= participants.getNumRows() - 1; i++) {
var email = participants.getValues()[i][0];