#!/bin/sh



############      SGE CONFIGURATION      ###################
# Write errors in the standard output file
#$ -j y 

# Shell to use
#$ -S /bin/bash

 #$ -b Y


# Mail to follow the exection of the job
#$ -M firstname.name@ird.fr           ######### change with your own email address

# Type of message to receive
#    -  (b) begining of the job
#    -  (e) end of the job
#    -  (a)  in case of abortion
#$ -m bea 

# Queue to use
#$ -q bioinfo.q
# To use serveral cores until 2
#$ -pe ompi 2
# Name of the job
#$ -N test_bwa_tando 
############################################################
 
### change the following values with yours 
path_to_dir="/data/projects/tp-cluster/training_2018/bwa";
path_to_tmp="/scratch/tando_$JOB_ID"; 
path_to_dest="/home/tando";

################ load bwa 0.7.12 anvironment########"#
module load bioinfo/bwa/0.7.12
 
###### Creation of a temporary folder on the chosen node
mkdir $path_to_tmp

####### Data copy to  the /scratch of the node
scp -r nas2:$path_to_dir $path_to_tmp # choose nas for /home, /data2 and /teams or nas2 for /data or nas3 pfor /data3
echo "tranfert donnees master -> noeud";
cd $path_to_tmp/bwa/;

###### Program execution
cmd1="bwa index referenceIrigin.fasta"; 
echo "commande executee: $cmd1";
$cmd1;
sleep 30

bwa mem referenceIrigin.fasta irigin1_1.fastq irigin1_2.fastq > mapping.sam 





##### Data transfer from node to nas
scp -rp $path_to_tmp/bwa/mapping.sam  nas:$path_to_dest/;
echo "Transfert donnees node -> master";

#### Deletion of the temporary folder in the /scratch of the node
rm -rf $path_to_tmp;
echo "Data deletion on node";