-
Notifications
You must be signed in to change notification settings - Fork 23
/
illumina_support_FC.sh
executable file
·73 lines (53 loc) · 2.35 KB
/
illumina_support_FC.sh
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
69
70
71
72
73
###
### This script allows to easily download from preproc1 the informaiton that is usually
### requested by Illumina tech support in order to troubleshoot an HiSeqX run
###
if [ $# -eq 3 ]; then
echo "Trying to retrive information for FC $1 from server $2 from user $3"
else
echo "You need to specify one FC (DATE_INSTRUM_RUN_FCID), a server ([email protected]), and a user name (name)"
fi
FC="$1"
server="$2"
user="$3"
if [ -d $FC ]; then
echo "FC $FC exists: aborting, delete before rerunning this"
exit 1
fi
mkdir $FC
echo " fetch xml info"
scp -r $user@$server:/srv/illumina/HiSeq_X_data/nosync/$FC/*xml $FC > $FC\_sync.out 2> $FC\_sync.err
echo " fetch csv info"
scp -r $user@$server:/srv/illumina/HiSeq_X_data/nosync/$FC/*csv $FC >> $FC\_sync.out 2>> $FC\_sync.err
echo " fetch std out and std err of commands (bcl2fastq and rsync)"
scp -r $user@$server:/srv/illumina/HiSeq_X_data/nosync/$FC/*.err $FC >> $FC\_sync.out 2>> $FC\_sync.err
scp -r $user@$server:/srv/illumina/HiSeq_X_data/nosync/$FC/*.out $FC >> $FC\_sync.out 2>> $FC\_sync.err
echo " fetch Logs dir"
scp -r $user@$server:/srv/illumina/HiSeq_X_data/nosync/$FC/Logs $FC >> $FC\_sync.out 2>> $FC\_sync.err
echo " fetch InterOp dir"
scp -r $user@$server:/srv/illumina/HiSeq_X_data/nosync/$FC/InterOp $FC >> $FC\_sync.out 2>> $FC\_sync.err
echo " fetch Config dir"
scp -r $user@$server:/srv/illumina/HiSeq_X_data/nosync/$FC/Config $FC >> $FC\_sync.out 2>> $FC\_sync.err
echo " fetch RTALogs dir"
scp -r $user@$server:/srv/illumina/HiSeq_X_data/nosync/$FC/RTALogs $FC >> $FC\_sync.out 2>> $FC\_sync.err
echo " fetch Recipe dir"
scp -r $user@$server:/srv/illumina/HiSeq_X_data/nosync/$FC/Recipe $FC >> $FC\_sync.out 2>> $FC\_sync.err
echo " fetch Demux dir"
scp -r $user@$server:/srv/illumina/HiSeq_X_data/nosync/$FC/Demultiplexing $FC >> $FC\_sync.out 2>> $FC\_sync.err
tar -zcvf $FC.tar.gz $FC >> $FC\_sync.out 2>> $FC\_sync.err
echo "The $FC.tar.gz contains:"
echo " - RunInfo.xml"
echo " - RTAConfiguration.xml"
echo " - runParameters.xml"
echo " - RTAConfiguration.xml"
echo " - SampleSheet.csv"
echo " - bcl2fastq.err (std err of bcl2fastq command)"
echo " - bcl2fastq.out (std out of bcl2fastq command)"
echo " - InterOp folder"
echo " - Logs folder"
echo " - Config folder"
echo " - RTALogs folder"
echo " - Recipe folder"
echo " - Demultiplexing folder"
echo ""
exit 0