johandahlberg

package molmed

import net.sf.samtools.util.SortingCollection
import net.sf.samtools.BAMRecordCodec
import net.sf.picard.fastq.FastqRecord
import java.util.Comparator
import java.io.InputStream
import java.io.PrintStream
import net.sf.picard.fastq.FastqConstants

johandahlberg

#!/bin/bash -l
#SBATCH -A b2010028
#SBATCH -p core
#SBATCH -n 2
#SBATCH -t 10:00:00
#SBATCH -J prepare_ref
#SBATCH -o prepare_ref-%j.out
#SBATCH -e prepare_ref-%j.error

# Author: Johan D

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 <- 

johandahlberg

# 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%;

johandahlberg

/*
* 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

---
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

# Licence:
# https://creativecommons.org/licenses/by/3.0/

library(ggplot2)
library(reshape2)
library(dplyr)

# Data:
# Downloaded at: http://www.statistikdatabasen.scb.se/pxweb/sv/ssd/START__HE__HE0110__HE0110A/SamForvInk2/?rxid=c58583e1-7fc3-418a-9395-0300e138fe7f
# Sammanräknad förvärvsinkomst, medianinkomst för boende i Sverige den 31/12, tkr efter region, kön, ålder och år

johandahlberg

echo "Time in container"
for i in $(seq 1 5)
do
    /usr/bin/time -f "time: %e" proot -S debian-sid --bind=/proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-13-3/03-BAM/ samtools mpileup -r 22:1-23096112  /proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-13-3/03-BAM/CEP-13-3.clean.dedup.recal.bam 2>&1 > test.pileup | grep time
done

echo "Time outside container"
for i in $(seq 1 5)
do
    /usr/bin/time -f "time: %e" samtools mpileup -r 22:1-23096112  /proj/a2009002/webexport/opendata/HiSeqX_CEPH/CEP-13-3/03-BAM/CEP-13-3.clean.dedup.recal.bam 2>&1 > test.pileup | grep time