#!/bin/bash
#SBATCH --dependency=afterany:11053:11054:11055:11056:11057:11058
set -e
set -o pipefail
umask 0002

#### SET THE STAGE
SCRATCH_DIR=/scratch/EdgeR_diff--over--undiff_2024-12-04--16-03-44_temp$$
GSTORE_DIR=/srv/GT/analysis/course_sushi/public/gstore/projects
INPUT_DATASET=/srv/GT/analysis/course_sushi/public/gstore/projects/p6003/EdgeR_diff--over--undiff_2024-12-04--16-03-44/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



#### NOW THE ACTUAL JOBS STARTS
module load Dev/R/4.4.0
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']] = '4'
param[['ram']] = '16'
param[['scratch']] = '10'
param[['partition']] = 'course'
param[['process_mode']] = 'DATASET'
param[['samples']] = 'S1_undiff,S2_undiff,S3_undiff,S4_diff,S5_diff,S6_diff'
param[['refBuild']] = 'Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30'
param[['refFeatureFile']] = 'genes.gtf'
param[['featureLevel']] = 'gene'
param[['testMethod']] = 'glm'
param[['deTest']] = 'QL'
param[['grouping']] = 'Condition'
param[['sampleGroup']] = 'diff'
param[['sampleGroupBaseline']] = ''
param[['refGroup']] = 'undiff'
param[['refGroupBaseline']] = ''
param[['onlyCompGroupsHeatmap']] = 'true'
param[['normMethod']] = 'TMM'
param[['grouping2']] = ''
param[['backgroundExpression']] = '10'
param[['transcriptTypes']] = 'protein_coding'
param[['pValueHighlightThresh']] = '0.01'
param[['log2RatioHighlightThresh']] = '0.5'
param[['runGO']] = 'true'
param[['pValThreshGO']] = '0.01'
param[['log2RatioThreshGO']] = '0'
param[['fdrThreshORA']] = '0.05'
param[['fdrThreshGSEA']] = '0.05'
param[['specialOptions']] = ''
param[['expressionName']] = ''
param[['mail']] = ''
param[['Rversion']] = 'Dev/R/4.4.0'
param[['sushi_app']] = 'EdgeRApp'
param[['comparison']] = 'diff--over--undiff'
param[['name']] = 'diff--over--undiff'
param[['dataRoot']] = '/srv/GT/analysis/course_sushi/public/gstore/projects'
param[['resultDir']] = 'p6003/EdgeR_diff--over--undiff_2024-12-04--16-03-44'
param[['isLastJob']] = TRUE
output = list()
output[['Name']] = 'diff--over--undiff'
output[['Species']] = 'Homo sapiens (human)'
output[['refBuild']] = 'Homo_sapiens/GENCODE/GRCh38.p13/Annotation/Release_42-2023-01-30'
output[['Static Report [Link]']] = 'p6003/EdgeR_diff--over--undiff_2024-12-04--16-03-44/diff--over--undiff/00index.html'
output[['Live Report [Link]']] = 'http://fgcz-shiny.uzh.ch/exploreDE?data=p6003/EdgeR_diff--over--undiff_2024-12-04--16-03-44/diff--over--undiff'
output[['Report [File]']] = 'p6003/EdgeR_diff--over--undiff_2024-12-04--16-03-44/diff--over--undiff'
input = '/srv/GT/analysis/course_sushi/public/gstore/projects/p6003/EdgeR_diff--over--undiff_2024-12-04--16-03-44/input_dataset.tsv'
EzAppEdger\$new()\$run(input=input, output=output, param=param)
EOT


#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP
rsync -r diff--over--undiff /srv/GT/analysis/course_sushi/public/gstore/projects/p6003/EdgeR_diff--over--undiff_2024-12-04--16-03-44/
cd /scratch
rm -rf /scratch/EdgeR_diff--over--undiff_2024-12-04--16-03-44_temp$$ || exit 1


echo __SCRIPT END__