Quick Start Guide

This guide will walk you through basic installation and usage of CAMPAREE, by running a simulation on a simplified dataset consisting of a mouse genome truncated to about 6 million bases and two samples of reads that align there. You can find more detailed installation instructions here.

Installation

Make sure you have the following installed on your system:

• git
• python version 3.10
• pip
• Java 1.8

Pull the git repo for CAMPAREE and BEERS_UTILS the into a convenient location:

git clone https://github.com/itmat/CAMPAREE.git
git clone https://github.com/itmat/BEERS_UTILS.git

Create a Python virtual environment to install required Python libraries. Note, if this command fails because your system doesn’t recognize the python3 command, you might need to run it with python instead:

cd CAMPAREE
python3 -m venv ./venv_camparee

Note, on your system Python 3 might be accessed using the ‘python’

And activate the environment:

source ./venv_camparee/bin/activate

Install required libraries:

pip install -r requirements.txt
pip install -r ../BEERS_UTILS/requirements.txt

Install CAMPAREE package in your Python environment:

pip install -e .

Next, install the BEERS_UTILS package that CAMPAREE uses:

pip install -e ../BEERS_UTILS

Baby Genome

The “baby genome” is a truncated version of mm10 consisting of segments of length at most 1 million bases chosen from chromosomes 1, 2, 3, X, Y, and MT.

Create STAR index for alignment to the baby genome:

bin/create_star_index_for_baby_genome.sh

Perform Test Run

We are now ready to run CAMPAREE on a two small sample fastq files aligning to the baby genome. If you have not already done so for installation, activate the python environment:

source ./venv_camparee/bin/activate

The default config file for the baby genome has CAMPAREE run all operations serially on a single machine. To perform the test with these defaults run:

bin/run_camparee.py -c config/baby.config.yaml -r 1

The argument -r 1 indicates that the run number is 1. If you run this again, you must either remove the output directory test_data/results/run_1/ or specify a new run number.

It is also possible to test deployment to a cluster. For LSF clusters run:

bin/run_camparee.py -c config/baby.config.yaml -r 1 -m lsf

For SGE clusters run:

bin/run_camparee.py -c config/baby.config.yaml -r 1 -m sge

Check Results

When the run completes, all output will be saved to CAMPAREE/test_data/results/run_1/. The final outputs will be in the text files test_data/results/run_1/CAMPAREE/data/sample1/molecule_file.txt and test_data/results/run_1/CAMPAREE/data/sample2/molecule_file.txt. Each line (after the header line) corresponds to the sequence of a single simulated molecule in a tab-delimited format. The default config file outputs 10000 molecules.

Validate the contents of these files by running the following md5sum command in the CAMPAREE install directory:

md5sum test_data/results/run_1/CAMPAREE/data/sample*/molecule_file.txt

The output of this command should match the following md5sum values:

835791fad7ee1d8c00d4285ffc166bb1  sample1/molecule_file.txt
03cb79060e9878e01c7ce4b64646f88d  sample2/molecule_file.txt