#!/bin/bash

set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p8002/PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41/input_dataset.tsv
LAST_JOB=TRUE
echo "Job runs on `hostname`"
echo "at $SCRATCH_DIR"
mkdir $SCRATCH_DIR || exit 1
cd $SCRATCH_DIR || exit 1
source /usr/local/ngseq/etc/lmod_profile
module add Dev/R/4.4.0

#### NOW THE ACTUAL JOBS STARTS
R --vanilla --slave<<  EOT
EZ_GLOBAL_VARIABLES <<- '/usr/local/ngseq/opt/EZ_GLOBAL_VARIABLES.txt'
if (!library(ezRun, logical.return = TRUE)){
message('retry loading ezRun')
Sys.sleep(120)
library(ezRun)
}
param = list()
param[['cores']] = '1'
param[['ram']] = '7'
param[['scratch']] = '10'
param[['partition']] = 'course'
param[['process_mode']] = 'DATASET'
param[['samples']] = '08_003_a,08_003_b,08_006_a,08_006_b,13_019_a,13_019_b,13_022_a,13_022_b'
param[['grouping']] = 'Medication'
param[['sampleGroup']] = 'after'
param[['refGroup']] = 'before'
param[['mail']] = ''
param[['sushi_app']] = 'PostSamsa2AnalysisApp'
param[['name']] = 'PostSamsa2Analysis'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p8002/PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = 'PostSamsa2Analysis'
output[['Report [File]']] = 'p8002/PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41/PostSamsa2Analysis'
output[['Static Report [Link]']] = 'p8002/PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41/PostSamsa2Analysis/00index.html'
input = '/srv/GT/analysis/course_sushi/public/gstore/projects/p8002/PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41/input_dataset.tsv'
EzAppPostSamsa2Analysis\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r PostSamsa2Analysis /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41/
cd /scratch
rm -rf /scratch/PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41_temp$$ || exit 1


echo __SCRIPT END__