Shane Hogle slhogle

Linkage Disequilibrium Calculation

This is complete taken from Ryan D on biostar: http://www.biostars.org/p/2909/#16419

It takes a region in a format like "chr2:1234-3456". If an rs number is specified after the region, it will output the R^2 for every SNP in that region with the requested SNP; otherwise, it is all-vs-all.

create private/public key combo

ssh-keygen -b 2048 -f mykeyname
create password

append public key to remote host

SSH to remote host
cd to ~/.ssh
append contents of public key file (mykeyname_rsa.pub) to ~/.ssh/authorized_keys

add to ssh-agent

Introduction

It was a pain to install cartopy on macOS. Here is what I did. It works as of Feb 10 2020. Uses proj, geos, and gdal from homebrew. none of that conda crap. Inspiration from here

Install your geo dependencies via homebrew

brew install proj  # version 6.3.0
brew install geos  # version 3.8.0
brew install gdal  # version 2.4.4

	#!/bin/bash

	nopts=$#

	# Bind common CSC environment directories
	SING_FLAGS="$SING_FLAGS -B /nobackup1:/nobackup1 -B /pool001:/pool001 -B /nfs:/nfs"

	# Bind TMPDIR if it is set and directory exists
	if [ -d "$TMPDIR" ]; then
	SING_FLAGS="$SING_FLAGS -B $TMPDIR:$TMPDIR"

	import os
	import urllib2
	import math

	def downloadChunks(url):
	"""Helper to download large files
	the only arg is a url
	this file will go to a temp directory
	the file will also be downloaded
	in chunks and print out how much remains