-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathsip.sh
More file actions
119 lines (77 loc) · 5.22 KB
/
Copy pathsip.sh
File metadata and controls
119 lines (77 loc) · 5.22 KB
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
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
#!/bin/bash
touch sip.log
exec > sip.log 2>&1
#===================================================
#=======================Primary=====================
#===================================================
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /home/ubuntu/loop_analyzer/data/GSE63525_GM12878_insitu_primary_30.hic /home/ubuntu/loop_analyzer/data/hg19.chrom.sizes /home/ubuntu/loop_analyzer/data/sip /home/ubuntu/loop_analyzer/data/juicer_tools_1.22.01.jar -cpu 7 -res 5000 -t 9000
end=$(date +%s)
echo "At 5K primary Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /home/ubuntu/loop_analyzer/data/GSE63525_GM12878_insitu_primary_30.hic /home/ubuntu/loop_analyzer/data/hg19.chrom.sizes /home/ubuntu/loop_analyzer/data/sip/primary/ /home/ubuntu/loop_analyzer/data/juicer_tools_1.22.01.jar -cpu 8 -res 10000
end=$(date +%s)
echo "At 10K primary Elapsed Time: $(($end-$start)) seconds"
#===================================================
#=======================Replicate=====================
#===================================================
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /home/ubuntu/loop_analyzer/data/GSE63525_GM12878_insitu_replicate_30.hic /home/ubuntu/loop_analyzer/data/hg19.chrom.sizes /home/ubuntu/loop_analyzer/data/sip/replicate/ /home/ubuntu/loop_analyzer/data/juicer_tools_1.22.01.jar -cpu 8 -res 5000
end=$(date +%s)
echo "At 5K replicate Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /home/ubuntu/loop_analyzer/data/GSE63525_GM12878_insitu_replicate_30.hic /home/ubuntu/loop_analyzer/data/hg19.chrom.sizes /home/ubuntu/loop_analyzer/data/sip/replicate/ /home/ubuntu/loop_analyzer/data/juicer_tools_1.22.01.jar -cpu 8 -res 10000
end=$(date +%s)
echo "At 10K replicate Elapsed Time: $(($end-$start)) seconds"
#===================================================
#=======================K562=====================
#===================================================
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /home/ubuntu/loop_analyzer/data/GSE63525_K562_combined_30.hic /home/ubuntu/loop_analyzer/data/hg19.chrom.sizes /home/ubuntu/loop_analyzer/data/sip/K562/ /home/ubuntu/loop_analyzer/data/juicer_tools_1.22.01.jar -cpu 8 -res 5000
end=$(date +%s)
echo "At 5K K562 Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /home/ubuntu/loop_analyzer/data/GSE63525_K562_combined_30.hic /home/ubuntu/loop_analyzer/data/hg19.chrom.sizes /home/ubuntu/loop_analyzer/data/sip/K562/ /home/ubuntu/loop_analyzer/data/juicer_tools_1.22.01.jar -cpu 8 -res 10000
end=$(date +%s)
echo "At 10K K562 Elapsed Time: $(($end-$start)) seconds"
#!/bin/bash
exec > sip.log 2>&1
#===================================================
#=======================Primary=====================
#===================================================
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /home/ubuntu/loop_analyzer/data/hub/GSE63525_GM12878_insitu_primary_30.hic ./hg19.chrom.sizes /home/ubuntu/loop_analyzer/data/hub/sip ./juicer_1.22.01.jar -res 5000 -t 9000
end=$(date +%s)
echo "primary @5k elapsed time: $(($end-$start)) seconds"
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /home/ubuntu/loop_analyzer/data/hub/GSE63525_GM12878_insitu_primary_30.hic ./hg19.chrom.sizes /home/ubuntu/loop_analyzer/data/hub/sip ./juicer_1.22.01.jar -res 10000 -t 9000
end=$(date +%s)
echo "primary @10k elapsed time: $(($end-$start)) seconds"
java -jar SIP_HiC_v1.6.1.jar hic /storage/store/mohit/data/GM12878_primary_30.hic hg19.chrom.sizes /storage/store/mohit/data/sip_result juicer_tools_1.13.01.jar -norm NONE
#!/bin/bash
touch sip.log
exec > sip.log 2>&1
#===================================================
#=======================Primary=====================
#===================================================
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /storage/store/mohit/data/GM12878_primary_30.hic hg19.chrom.sizes /storage/store/mohit/data/sip juicer_tools_1.13.01.jar -norm NONE
end=$(date +%s)
echo "primary @5k, Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /storage/store/mohit/data/GM12878_primary_30.hic hg19.chrom.sizes /storage/store/mohit/data/sip juicer_tools_1.13.01.jar -norm NONE -res 10000
end=$(date +%s)
echo "primary @10k, Elapsed Time: $(($end-$start)) seconds"
#===================================================
#=====================Replicate=====================
#===================================================
#!/bin/bash
exec > sip.log 2>&1
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /storage/store/mohit/data/GSE63525_GM12878_insitu_replicate_30.hic hg19.chrom.sizes /storage/store/mohit/data/replicate/sip juicer_tools_1.13.01.jar -norm KR -res 5000
end=$(date +%s)
echo "replicate @5k, Elapsed Time: $(($end-$start)) seconds"
start=$(date +%s)
java -jar SIP_HiC_v1.6.1.jar hic /storage/store/mohit/data/GSE63525_GM12878_insitu_replicate_30.hic hg19.chrom.sizes /storage/store/mohit/data/replicate/sip juicer_tools_1.13.01.jar -norm KR -res 10000
end=$(date +%s)
echo "replicate @10k, Elapsed Time: $(($end-$start)) seconds"