#!/bin/sh

# ACE

#################
# PBS VARIABLES #
#################

#PBS -V
#PBS -N velvet
#PBS -e pbs.err
#PBS -o pbs.out
#PBS -r n
##PBS -q <low_mem|mid|mem|high_mem|regular|workq>
#PBS -q high_mem
##PBS -l <free|pack|scatter|vscatter>
#PBS -l place=scatter
##PBS -l select=<1-12>:ncpus=<1-64>:mpiprocs=<1-64>:mem=<gb>:host=<n001-n012>
#PBS -l select=1:ncpus=64:mpiprocs=64:mem=512:host=n009
#PBS -l walltime=8760:00:00
# FABRIC=<shm|sock|ssm|rdma|rdssm>
FABRIC=rdma
CORES=$[ `cat $PBS_NODEFILE | wc -l` ]
NODES=$[ `uniq $PBS_NODEFILE | wc -l` ]
cd $PBS_O_WORKDIR

###################
# LOG AND MODULES #
###################

printf "Time =  `date`\n" > $PBS_JOBNAME-$PBS_JOBID.jobinfo
printf "PBS work directory = $PBS_O_WORKDIR\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
printf "PBS queue = $PBS_O_QUEUE\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
printf "PBS job ID = $PBS_JOBID\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
printf "PBS job name = $PBS_JOBNAME\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
printf "Fabric interconnect selected = $FABRIC\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
printf "This job will run on $CORES processors\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
printf "List of nodes in $PBS_NODEFILE\n\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
uniq $PBS_NODEFILE >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
. /etc/profile.d/modules.sh
module load mpt && printf "\n\nSuccessfully load modules\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
printf "mpiexec_mpt run command location = `which mpiexec_mpt`\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
printf "\n[START] qstat -f $PBS_JOBID\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
qstat -f $PBS_JOBID >> $PBS_JOBNAME-$PBS_JOBID.jobinfo
printf "\n[END] qstat -f $PBS_JOBID\n" >> $PBS_JOBNAME-$PBS_JOBID.jobinfo

###########
# COMMAND #
###########

## TEMPLATE FOR MPIEXEC:
# mpiexec_mpt -n $CORES <program/path> <arguments> <stderr> 2> <stdout>

## EXAMPLES:
# mpiexec_mpt -n $CORES /apps/poy511bs2_mpi -e script.poy > stderr 2> stdout
# /apps/mira manifest.conf > mira.log

# Temporarily add ZLIB 1.2.8 to LD_LIBRARY_PATH:
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/apps/ZLIB128/lib
export LD_LIBRARY_PATH

# Temporarily add VELVET1210 to PATH:
PATH=$PATH:/apps/:/apps/VELVET1210/
export PATH

# Environmetal variables for velveth and velvetg
export OMP_NUM_THREADS=63
export OMP_THREAD_LIMIT=64

# Preprocessing the sequences file before running the hashing
# Velvet will test all k-mer lengths equal or greater than 21 and smaller than 65 with a step of 2
/apps/VELVET1210/velveth output_dir/ 21,65,2 -fastq.gz -short ../se.fastq.gz -shortPaired -separate ../pe1.fastq.gz ../pe2.fastq.gz -shortPaired2 -separate ../mp1.fastq.gz ../mp2.fastq.gz -create_binary -noHash > preproc.stderr 2> preproc.stdout

# Hashing after pre-processing sequences
# Velvet will test all k-mer lengths equal or greater than 21 and smaller than 65 with a step of 2
/apps/VELVET1210/velveth output_dir/ 21,65,2 -fastq.gz -short ../se.fastq.gz -shortPaired -separate ../pe1.fastq.gz ../pe2.fastq.gz -shortPaired2 -separate ../mp1.fastq.gz ../mp2.fastq.gz -create_binary -reuse_Sequences > velveth.err 2> velveth.out

# Quickly obtain a decent assembly in your first run for k-mer 21
/apps/VELVET1210/velvetg auto_63 -exp_cov auto -cov_cutoff auto -shortMatePaired2 yes > velvetg.out 2> velvetg.err

# Reset LD_LIBRARY_PATH:
export LD_LIBRARY_PATH=/usr/lib64/jvm/jre-1.6.0-sun/lib/amd64/server:/usr/lib64/jvm/jre-1.6.0-sun/lib/amd64:/opt/sgi/sgimc/lib

# Reset PATH:
export PATH=/home/denis/perl5/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/lib/mit/sbin:/opt/sgi/sgimc/bin:.:/usr/local/boost:/usr/local/boost/lib:/usr/local/boost/include