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
|
#!/bin/bash
#Needs fastq-dump from the SRA toolkit to directly get the 100 raw fastq reads
fastq-dump -X 100 -Z SRR14953521 | head -n100 > data.fastq
mkdir -p data
if [ -f data/data.fastq.gz ]
then
gunzip data/data.fastq.gz
diff -u data.fastq data/data.fastq
if [ `echo $?` -ne 0 ]
then
echo "The data has changed, injecting new data, please check manually before upload"
else
echo "The data is same, no changes needed"
fi
fi
gzip data.fastq
rm data/data.fastq
mv data.fastq.gz data/data.fastq.gz
echo "Done"
|
