SraDownloadPBS.pl

#!/usr/bin/perl -w
# This is most complicated situation for RRBS or BS alignment since both single end and pair-end fastq were created in a project.
# Run the script to the Bam directory of the bismark
# Contact: Shicheng Guo
# Version 1.3
# Update: Jan/19/2016

use strict;
use Cwd;
my $dir=getcwd;
die "Usage: perl $0 SamConfig.txt submit_or_not[submit/no]\nPlease Download SamConfig from http://www.ebi.ac.uk/ena/data/view/SRP028600\n" if scalar(@ARGV<1);
my $sraFiles=shift @ARGV;
my $submit=shift @ARGV;
my $project="Fastq";
my $analysis="";
my $ppn=1;
my $walltime="168:00:00";
my $queue="hotel"; # hotel

open F,$sraFiles;
while(<F>){
    chomp;
    next if /SRRID/;
    next if /^\s+$/;
    my @line = split /\t/; 
    my $SRR_column;    
    foreach my $line(@line){
    $SRR_column++;
    if($line=~/SRR/){
    last;
    }
    }
    my $id=$line[$SRR_column-1];
    print "$id\n";
    # next if -e "$id.fastq.gz"; # SRR1035764.fastq.gz
    my $job_file_name = $id . ".job";
    my $status_file = $id.".status";
    my $curr_dir = $dir;
    open(OUT, ">$job_file_name") || die("Error in opening file $job_file_name.\n");
    print OUT "#!/bin/csh\n";
    print OUT "#PBS -N $id\n";
    print OUT "#PBS -q $queue\n";  # glean is free, pdafm
    print OUT "#PBS -l nodes=1:ppn=$ppn\n";
    print OUT "#PBS -l walltime=$walltime\n";
    print OUT "#PBS -o ".$id.".log\n";
    print OUT "#PBS -e ".$id.".err\n";
    print OUT "#PBS -V\n";
    print OUT "#PBS -M shicheng.guo\@gmail.com \n";
    print OUT "#PBS -m abe\n";
    print OUT "#PBS -A k4zhang-group\n";
    print OUT "cd $curr_dir\n";
    print OUT "fastq-dump --split-files --gzip $id\n";    
    close(OUT);
    if($submit eq 'submit'){
    system("qsub $job_file_name");
   }
}