1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_gangstr.sh
## Version : 0.0.1
## Licence : FIXME
## Description : a wrapper for qsubing STRScan script for STR detection
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_strscan.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191115
## last revision date : 20191115
## Known bugs : None
# Log file path option
if [ -z "$LOGFILE" ]
then
LOGFILE=strscan.$(date +"%F_%H-%M-%S").log
fi
# Logging
exec 1>> "$LOGFILE" 2>&1
echo "$(date +"%F_%H-%M-%S"): START"
# Check if input file exists
if [ ! -f "$INPUTFILE" ]
then
echo "Input file '$INPUTFILE' does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch strscan.failed
exit 1
fi
# Check if output prefix is specified
if [ -z "$OUTPUTPREFIX" ]
then
echo "Output prefix is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
touch strscan.failed
exit 1
fi
# Launch script command and check exit code
echo "command : /work/gad/shared/bin/strscan/STRScan_2019-11-05/STRScan \
-i "$INPUTFILE" \
-p /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
-o "$OUTPUTFILE""
/work/gad/shared/bin/strscan/STRScan_2019-11-05/STRScan \
-i "$INPUTFILE" \
-p /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
-o "$OUTPUTFILE"
strscan_exitcode=$?
echo "strscan exit code : $strscan_exitcode"
if [ $strscan_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
touch gangstr.failed
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"