#!/usr/local/bin/python

#pipeline_dir = '/data/kinney/jkinney/github/14_crispr'
#python_to_use = '/opt/hpc/pkg/python-2.7/bin/python'
#input_dir = '/data/kinney/jkinney/github/14_crispr/example'

pipeline_dir = '/Users/jkinney/github/14_crispr'
python_to_use = '/usr/local/bin/python'
input_dir = '/Users/jkinney/github/14_crispr/example'

# Indicate whether to use multiple nodes
use_multiple_nodes = False

# Give names of fastq files as a glob. 
read1_file_glob = input_dir + '/reads/r1_*.fastq'
read2_file_glob = input_dir + '/reads/r2_*.fastq'

experiments_file = input_dir + '/experiments.txt'
barcodes_file = input_dir + '/barcodes.txt'
regions_file = input_dir + '/regions.txt'
infection_file = input_dir + '/infection_rates.txt'

output_dir = input_dir + '/output'
reads_dir = output_dir + '/reads'
scripts_dir = output_dir + '/scripts'
results_dir = output_dir + '/results'
summary_dir = output_dir + '/summaries'
plots_dir = output_dir + '/plots'
efficiency_file = output_dir + '/efficiencies.txt'

# Run the pipeline
execfile(pipeline_dir+'/pipeline.py')
