#!/bin/bash

CORES=8
MAX_MEM="18GB"

set -e;

function actually_run_the_alignment {
    module load sratoolkit/2.3.5-2;
    module load bwa/0.7.10;
    module load cufflinks/2.2.1;
    module load samtools/1.0;
    (cd "${FROM_SRR_SRR}";
     fastq-dump --gzip ${FROM_SRR_SRR}.sra;
     bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam -;
     samtools sort ${FROM_SRR_SRR}.bam -o ${FROM_SRR_SRR}.sorted.bam -T temp
     cufflinks -p ${MAX_MEM} -G $FROM_SRR_GTF ${FROM_SRR_SRR}.sorted.bam;
     rm -f ${FROM_SRR_SRR}.fastq.gz ${FROM_SRR_SRR}.bam
    );
};

function set_up_the_run {
    FROM_SRR_SRR="$1"
    FROM_SRR_REF="$2"
    FROM_SRR_GTF="$3"
    export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
    mkdir -p "$FROM_SRR_SRR";
    (cd "$FROM_SRR_SRR";
     rsync -avP rsync://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/${FROM_SRR_SRR:0:6}/${FROM_SRR_SRR}/${FROM_SRR_SRR}.sra .;
    );
    qsub -q budget -v FROM_SRR_SRR,FROM_SRR_GTF,FROM_SRR_REF -S /bin/bash -d $(pwd) -m a -M donarm@illinois.edu -l "nodes=1:ppn=${CORES},mem=${MAX_MEM}" "$0"    
};


if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]; then
    if [ -n "$FROM_SRR_SRR" ]; then
        actually_run_the_alignment;
        exit 0;
    fi;
else
    set_up_the_run "$1" "$2" "$3";
    exit 0;
fi;
echo "You need to give an SRR, REF, and GTF on the command line";
exit 1;