#!/bin/bash
#
# Example data staging job script that copies a directory from Datastore to Eddie with rsync
#
# Job will restart from where it left off if it runs out of time
# (so setting an accurate hard runtime limit is less important)

# Grid Engine options start with a #$
#$ -N stageout_Log        
#$ -cwd   
# Choose the staging environment
#$ -q staging 

# Hard runtime limit
#$ -l h_rt=01:00:00   

# Make the job resubmit itself if it runs out of time: rsync will start where it left off
#$ -r yes 
#$ -notify
trap 'exit 99' sigusr1 sigusr2 sigterm #POSIX signals

#$ -t 1-2 #array 
# Source and destination directories

# SAMPLE is the name from the samples.txt list. From this base name bellow add the parts of the path that are the same for all samples, and leave "$SAMPLE" as the variable name. 
#ID file
IDFILE=/exports/eddie/scratch/$USER/Chimeras/Data/samples_last2Met.txt
# Assigning SAMPLE variable from the built-in array counter
SAMPLE=`sed -n ${SGE_TASK_ID}p "$IDFILE"`

SOURCE=/exports/cmvm/eddie/scs/groups/Williamsdata/Chimeras/outs/filter_70/CellRanger-onlyCB/human/$SAMPLE

DESTINATION=/exports/cmvm/datastore/scs/groups/Williamsdata/Nina/Chimeras/outs/filter_70/CellRanger-onlyCB/human

# Perform copy with rsync
# Note: do not use -p or -a (implies -p) as this can break file ACLs at the destination
#rsync -rl --remove-source-files ${SOURCE} ${DESTINATION}
mkdir -p $DESTINATION
rsync -rl ${SOURCE} ${DESTINATION}