WISECONDOR on autopilot: run.sh

The "I have no clue how to do this"-approach

As it turns out, lots of people with no to barely any knowledge about linux, terminals and anything to do with it want to be able to run WISECONDOR, I tried to add a simplification script to do most of the work by itself. It removes all possible options of the scripts and just runs everything in default settings. From what I've heard these settings work quite well so you can try it to see if the scripts work for your purposes.

What do I need to do?

Install Ubuntu or a Ubuntu based linux distribution. Although slow computers result in slow analysis, the scripts were able to run on a netbook when I developed them. If you cannot get your hands on a machine that can be wiped completely, you may look into virtual machines instead.

Installing Ubuntu is not rocket science: if you cannot do it yourself, the average Computer Science student should be able to do it for you. It's not expensive to get a working solution.

This script assumes you have the root password, meaning you are in full control of the machine. Although a bit dodgy if you do not know what you are doing, I assume you have a (virtual) machine running Ubuntu just for the purpose of running this software. If the packages are already installed, the script will not ask you for root permission anymore.

What does it do?

For every step, it tests if the result already exists. If so, the step is skipped. If not, it is applied:

1. It obtains the necessary packages using apt-get commands. This is the default package manager on Ubuntu systems and contains everything necessary to run WISECONDOR.
2. It creates a basic directory structure to accommodate differentation between sample purposes and data.
3. It creates a gccount file based on the fasta file provided in ./dataFiles/.
4. It creates a reference table file based on samples in ./refSamples/, converting from bam files where necessary.
5. It tests every sample in ./testSamples/, converting from bam files where necessary. Output is found as in ./testSamples/ as .pdf .plot .json

How do I use it?

Short answer

1. Turn your samples into sorted .bam files.
2. ./run.sh.
3. Follow remarks if it complains.
4. See step 2.

More extensive answer

0. Open a terminal.
1. Change to the directory you put WISECONDOR in: cd ./wisecondor/.
2. Run it: ./run.sh.
3. Enter root (sudo) password if it tells you to.
4. Put reference *.fasta file in ./dataFiles.
5. Put sorted reference sample *.bam and *.bai files in ./refSamples.
6. Put sorted test sample *.bam and *.bai files in ./testSamples.
7. Run it: ./run.sh.
8. Wait until it tells you it's finished. If it complains, see short answer.
9. Find your results in ./testSamples.
10. Open ./view.html in a webbrowser, preferrably chrome.
11. Load any of the *.json files in ./testSamples.