Dinh/Dinh 2013/NOTES/2013-1-7
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bisReadMapper pipeline
Triton
- Write a shell script as follows:
# current directory: change the following path to your working directory. cur_dir="/oasis/triton/scratch/ddiep/Working/WGBS_Noi_hg19/HELLO" # reads directory: change the following path to the reads directory # reads_dir and cur_dir doesn't have to be the same reads_dir="/oasis/triton/scratch/ddiep/Working/WGBS_Noi_hg19/HELLO" # the following paths should stay the same on triton. bisReadMapper="/home/ddiep/scripts/MethylationPipeline/smartBisReadMapper.pl" template_fwd="/projects/zhang-lab/ddiep/LatestGenome/bisHg19/hg19.fa.bis.fwd.index" template_rev="/projects/zhang-lab/ddiep/LatestGenome/bisHg19/hg19.fa.bis.rev.index" template_fa="/projects/zhang-lab/ddiep/LatestGenome/bisHg19/hg19.fa" soap="/home/ddiep/softwares/soap2.21release/soap" cd $cur_dir INDX="Indx1 Indx2 Indx3" for n in ${INDX} do f="s_1_1_$n.txt" g="s_1_2_$n.txt" echo "#!/bin/csh" > $n.job echo "#PBS -q small" >> $n.job echo "#PBS -l nodes=1:ppn=8" >> $n.job echo "#PBS -l walltime=36:00:00" >> $n.job echo "#PBS -o $n.log" >> $n.job echo "#PBS -e $n.err" >> $n.job echo "#PBS -V" >> Idx$n.job echo "#PBS -M diep.hue.dinh@gmail.com" >> $n.job echo "#PBS -m abe" >> $n.job echo "#PBS -A zhang-lab" >> $n.job echo "cd $cur_dir" >> $n.job echo "$bisReadMapper -r $reads_dir/$f,$reads_dir/$g -m 2 -W $template_fwd -C $template_rev -g $template_fa -a $soap -b 33 -p 8 -n $n -q 20 > $n.status" >> $n.job echo "rm *encoded" >> $n.job qsub $n.job done