btseq_align

#!/bin/tcsh -f

set defs = BSTarget_input.txt
set outdir = `pwd`
mkdir ${outdir}/Run
touch ${outdir}/Run/Run.q
chmod +x ${outdir}/Run/Run.q 
echo '#! /bin/sh' >> ${outdir}/Run/Run.q
cat $defs | awk -v d=${outdir} '{Qout=d "/Run/" $2 "_" $1 ".q"; print "touch " d "/Run/" $2 "_" $1 ".q\n" \\
"echo \047\043\\\041/bin/sh\047 >> " Qout "\n" \\
"echo echo \\$HOSTNAME >> " Qout "\n" \\
"echo mkdir " d "/" $2 "_" $1 ">> " Qout "\n" \\
"echo cp -s " $4 " " d "/" $2 "_" $1 " >> " Qout "\n" \\
"echo bismark_genome_preparation --bowtie2 " d "/" $2 "_" $1 " >> " Qout "\n" \\
"echo bismark " d "/" $2 "_" $1 " " $3 " --bowtie2 -o " d "/" $2 "_" $1 "/Output --temp_dir " d "/" $2 "_" $1 "/Output >> " Qout "\n" \\
"echo /cs/icore/joshua.moss/scripts/btseq/Analyze_Result.csh " $3 " " d "/" $2 "_" $1 " >> " Qout "\n" \\
"echo sbatch --job-name=aln --mem=4GB --cpus-per-task=3 --time=5:00:00 --output=" d "/Run/" $2 "_" $1 ".q.out " d "/Run/" $2 "_" $1 ".q >> " d "/Run/Run.q"}' | tcsh >& /dev/null

#echo Go to Run folder
${outdir}/Run/Run.q
echo Alignment has begun
# In the end run the following to zip the results:
#foreach n (`cat Def.txt | awk '{print $2}' | sort | uniq`)
#zip ${n}_Results `du -a | grep -P 'summary$|hist$' | grep ${n} | awk '{print $2}'`
#end