johandahlberg

library(ggplot2)
library(reshape2)
library(maps)

# A tab separated file with contries and participats.
# Note that Unites States needs to be changed to USA and United Kingdom
# to UK.
path.to.contry.and.participants.file <- "~/Desktop/contries.csv"

participants <- 

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# Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;

# Define a server that listens on port 3838
server {
  listen 3838;

  # Define a location at the base URL
  location / {

johandahlberg

<link rel="import" href="../polymer/polymer.html">

<polymer-element name="my-element">

  <template>
    <style>    
      :host {
        position: absolute;
        width: 100%;
        height: 100%;

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/*
* Copyright (c) 2012 The Broad Institute
* 
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following

johandahlberg

package example

import org.apache.spark.{SparkConf, SparkContext}
import org.apache.spark.rdd.RDD
import org.bdgenomics.adam.rdd.ADAMContext
import org.bdgenomics.formats.avro.NucleotideContigFragment

/**
 * Created by dahljo on 7/14/15.
 */

johandahlberg

package net.sf.picard.sam;

import java.io.BufferedReader;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStreamReader;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

johandahlberg

*----------------------------------
* Setting up git
*----------------------------------

Clone gatk git repo

Add the main gatk repo as a upstream remote repo:
git remote add upstream https://github.com/broadgsa/gatk.git

Change the remote of the master branch to upstream. .git/config should look like this.

johandahlberg

#!/usr/bin/python

import os

def get_immediate_subdirectories(dir):
    return [name for name in os.listdir(dir)
            if os.path.isdir(os.path.join(dir, name))]

# Get runfolder name from file and return as list.
def get_runfolders_already_run(file):

johandahlberg

---
title: Understanding the Rwandan genocide of 1994 through data from the Uppsala Conflict
  Data Program
author: "Johan Dahlberg"
date: "October 27, 2015"
output: html_document
licence: http://creativecommons.org/licenses/by-sa/3.0/
---

``` {r, echo=FALSE, message=FALSE}

johandahlberg

import scala.math.Ordering

object SimpleBW extends App {

    def bwt(s: String): String = {
        def tranformString(string: String): List[String] = { transformString(string, string.length) }

        def transformString(string: String, splitIndex: Int): List[String] = {
            if (splitIndex == 0) {
                // Recursion base case