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var webPage = require('webpage');
var fs = require('fs');
var page = webPage.create();

var urls = fs.read("fulltext_html_urls.txt").split("\n");
urls = urls.splice(0, urls.length - 1);

var ar_regex = /([0-9]+$)/;

console.log("scraping " + urls.length + " URLs");

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---
title: "test"
author: "Richard Smith-Unna"
date: "21 May 2015"
output: html_document
---
 
Demo of reading an R file and dumping it raw into the HTML produced by knitr from RMarkdown, to get syntax highlighting.
 
Put the code you want to display in `import.R`.

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#!/bin/sh

# this is a modified WildFly standalone startup script. It launches the
# server in the background, and instead of the script running until the server
# exits, the script runs until it receives a kill signal (leaving the server
# running in the background).
#
# This allows you to monitor the script output and decide when to kill it. For
# example if you wanted to only exit the script once the server has
# successfully launched, you could do:

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#! /usr/bin/env ruby

# This is a game that helps people understand genome assembly. Given a string,
# it generates sequence reads giving perfect coverage of the string and with a
# fixed overlap. The idea is to print the generated reads, cut them out, and
# have learners assemble them by hand. Different difficulties can be
# demonstrated by using a string with repeats, low complexity, etc., to mimic
# real assembly problems, or by adjusting the parameters (overlap and number
# of fragments).

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{
  "type": "article",
  "publisher": {
    "name": "Public Library of Science (PLoS)"
  },
  "journal": {
    "issn": "1932-6203",
    "name": "PLoS ONE",
    "volume": "1",
    "issue": "5",

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Title: Unix Primer for Biologists Authors: Keith Bradnam & Ian Korf Date: September 27, 2012 Web: unixandperl.com Address: Genome Center, UC Davis, Davis, CA, 95616

Unix and Perl Primer for Biologists

Keith Bradnam & Ian Korf

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## ContentMine VM setup script

echo password | sudo -S apt-get update -y

## Java 7
sudo apt-get install -y openjdk-7-jdk
sudo update-alternatives --config java
sudo update-alternatives --config javac

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[WARNING] Assembly file: /home/vagrant/ami2-poc/target/ami2-poc-0.0.2-SNAPSHOT-bin is not a regular file (it may be a directory). It cannot be attached to the project build for installation or deployment.
[INFO]
[INFO] --- jdeb:1.3:jdeb (default) @ ami2-poc ---
Downloading: http://repo.maven.apache.org/maven2/javax/annotation/jsr250-api/1.0/jsr250-api-1.0.jar
Downloading: http://repo.maven.apache.org/maven2/com/google/guava/guava/10.0.1/guava-10.0.1.jar
Downloading: http://repo.maven.apache.org/maven2/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar
Downloaded: http://repo.maven.apache.org/maven2/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar (33 KB at 230.3 KB/sec)
Downloaded: http://repo.maven.apache.org/maven2/javax/annotation/jsr250-api/1.0/jsr250-api-1.0.jar (0 B at 0.0 KB/sec)
Downloaded: http://repo.maven.apache.org/maven2/com/google/guava/guava/10.0.1/guava-10.0.1.jar (1467 KB at 2242.2 KB/sec)
[INFO] Creating debian package: /home/vagrant/ami2-poc/target/ami2-poc_0.0.2~SNAPSHOT_all.deb

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Transrate assembly and contig plots.
========================================================

Assemblies of mouse with 10, 20, 50 and 100 million reads.

# Assembly-level stats

## Load data

```{r}

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set_prompt () {
    Last_Command=$? # Must come first!
    Blue='\[\e[01;34m\]'
    White='\[\e[01;37m\]'
    Red='\[\e[01;31m\]'
    Green='\[\e[01;32m\]'
    Reset='\[\e[00m\]'
    FancyX='\342\234\227'
    Checkmark='\342\234\223'