alexharkess

#!/usr/bin/perl
use strict;
use warnings;

open IN, '<', "readlist.txt";
while (<IN>) {
    my ($left, $prefix) = split /\s+/, $_;
    open OUT, '>', "$prefix.trim.sh";
    print OUT "java -jar /usr/local/trimmomatic/latest/trimmomatic-0.32.jar SE -phred33 -threads 2 $left $prefix\.clean.fq.gz ILLUMINACLIP:/usr/local/trimmomatic/latest/adapters/TruSeq2-PE.fa:2:30:10 LEADING:10 TRAILING:10 MINLEN:50";
    system "qsub -q rcc-30d -pe thread 2 $prefix.trim.sh";

alexharkess

#!/usr/bin/perl
use strict;
use warnings;

my @fastqs = <*fastq.gz>;
my $files = join (" ", @fastqs);

open OUT, '>', "all_fastqc.sh";

print OUT "#!/bin/bash\n";

alexharkess

[clustalw2]
args =
path = /panfs/pstor.storage/rcclocal/zcluster/pasta/1.6.3/bin/clustalw2

[commandline]
aligned = False
datatype = DNA
keepalignmenttemps = False
keeptemp = False
multilocus = False