enqueue_pipeline.sh 820 Bytes
Newer Older
Chris Jewell's avatar
Chris Jewell committed
1
2
3
4
#!/bin/bash

# Enqueues COVID-19 pipelines

5
6
7
8
CASES_FILE="data/Anonymised Combined Line List 20210108.csv"
COMMUTE_VOL_FILE="data/210108_OFF_SEN_COVID19_road_traffic_national_table.xlsx"
DATE_LOW="2020-10-13"
DATE_HIGH="2021-01-05"
Chris Jewell's avatar
Chris Jewell committed
9
10
11
12
13
14
15

TEMPLATE_CONFIG=template_config.yaml


# Job submisison
switch-gpu

16
for PILLAR in both 1 2
Chris Jewell's avatar
Chris Jewell committed
17
do
18
    for CASE_DATE_TYPE in specimen
Chris Jewell's avatar
Chris Jewell committed
19
    do
Chris Jewell's avatar
Chris Jewell committed
20
21
22
23
	RESULTS_DIR=$global_scratch/covid19/${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}
	JOB_NAME="covid_${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}"	
	qsub -N $JOB_NAME covid_pipeline.sge \
	     --reported-cases "$CASES_FILE" \
24
	     --commute-volume "$COMMUTE_VOL_FILE" \
Chris Jewell's avatar
Chris Jewell committed
25
26
	     --case-date-type $CASE_DATE_TYPE \
	     --pillar $PILLAR \
27
	     --date-range $DATE_LOW $DATE_HIGH \
Chris Jewell's avatar
Chris Jewell committed
28
	     --results-dir "$RESULTS_DIR" \
29
	     --config $TEMPLATE_CONFIG
Chris Jewell's avatar
Chris Jewell committed
30
31
    done
done