#!/bin/bash
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#Andy Rampersaud, 01.27.16
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#Assumptions for this job to run correctly:
#Your data is organized in the following way:
#You have a data set dir such as:
#wax-es/aramp10/G83_Samples
#Within this dir you have sample specific folders such as:
#G83_M1
#G83_M2
#G83_M3
#G83_M4
#Within each sample specific folder you have a "fastq" folder with:
#Files: *_R1_*.fastq.gz and *_R2_*.fastq.gz such as:
#Waxman-TP17_CGATGT_L007_R1_001.fastq.gz
#Waxman-TP17_CGATGT_L007_R2_001.fastq.gz
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#Fill in the following information:
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#Information about your data set
#As mentioned above, you should have a data set dir containing your sample specific folders:
#Dataset_DIR=/projectnb/wax-es/aramp10/G83_Samples
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#Samples to process
#To facilitate processing of samples in parallel we can use a text file that lists the samples to analyze
#Note: this text file is still valid even if there is only one sample to process
#You need to have a "Sample_Labels" dir within your Dataset_DIR
#Within the Sample_Labels dir have a Sample_Labels.txt such that:
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#The text file is formatted like the following:
#----------------------------------------------
#Sample_DIR	Sample_ID	Description
#Sample_Waxman-TP17	G83_M1	Male 8wk-pool 1
#Sample_Waxman-TP18	G83_M2	Male 8wk-pool 2
#Sample_Waxman-TP19	G83_M3	Female 8wk-pool 1
#Sample_Waxman-TP20	G83_M4	Female 8wk-pool 2
#----------------------------------------------
#The 1st column: The Sample_DIR name
#The 2nd column: Waxman Lab Sample_ID 
#The 3rd column: Sample's description 
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#Sample_Labels_DIR=${Dataset_DIR}/Sample_Labels
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#Time hour limit
#On SCC a 12-hour runtime limit is enforced on all jobs, unless specified explicitly. 
#A runtime limit can be specified in the format "hh:mm:ss"
#Dont change the following time limit value unless you know that your job is going to go over 12 hrs 
#TIME_LIMIT="12:00:00"
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