-
Notifications
You must be signed in to change notification settings - Fork 4
/
smrtlink_on_nci
143 lines (103 loc) · 4.76 KB
/
smrtlink_on_nci
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
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
module load python 3.6.2
mkdir -p /short/sd34/ap5514/myapps/smrtlink/5.1.0
export PYTHONPATH=/short/sd34/ap5514/myapps/smrtlink/5.1.0/lib/python3.6/site-packages
mkdir -p $PYTHONPATH
export PATH=/short/sd34/ap5514/myapps/smrtlink/5.1.0/bin:$PATH
cd /short/sd34/ap5514/myapps/smrtlink/5.1.0
wget https://downloads.pacbcloud.com/public/software/installers/smrtlink_5.1.0.26412.zip
unzip smrtlink_5.1.0.26412.zip
#enter unzip password from website
#enter root directory
SMRT_ROOT=/short/sd34/ap5514/myapps/smrtlink/5.1.0
smrtlink_5.1.0.26412.run --rootdir $SMRT_ROOT
----- Part 1 of 10: SMRT Analysis User ----
It is recommended to run this script as a designated SMRT Analysis
user (e.g. smrtanalysis) who will own all smrtpipe jobs and daemon
processes.
Current user is 'ap5514' (primary group: sd34)
Use the 'ap5514' as the SMRT Analysis user? [Y/n]: y
Using install user (computed): ap5514
Using install group (computed): sd34
Using smrtlink uuid (computed default): f3b0ec25-8db7-4adf-92fd-2762e40985c6
----- Part 2 of 10: SMRT Link Server DNS -----
The DNS name of the SMRT Link host server is used for creating SMRT
Link URLs (e.g. http://smrtlink.example.com:9090), ensuring
an SSL certificate will validate. If the Domain Name System (DNS)
does not resolve to the expected address, then an IP address must
be used.
Detecting DNS names...
----- Part 3 of 10: SMRT Link Setup ----
SMRT Link requires two ports for proper operation. These ports cannot
be used for listening by any other processes. The SMRT Link GUI port
serves to redirect from an unencrypted http connection to the login
page using secure https.
Enter the SMRT Link GUI (http) port [9090]: 9090
Enter the SMRT Link Services port [9091]: 9091
Memory settings must be preset for SMRT Link. By default, we set the
initial (-Xms) and maximum (-Xmx) Java heap sizes to the same values.
The default for SMRT Link services is 25% of the total memory with a
maximum of 32768 MB. The default for SMRT Link GUI is 5% of the total
memory with a maximum of 8192 MB. We recommend using the defaults.
Enter the SMRT Link Services initial memory (in MB) [25088]:
Enter the SMRT Link Services maximum memory (in MB) [25088]:
Enter the SMRT Link GUI initial memory (in MB) [4992]:
Enter the SMRT Link GUI maximum memory (in MB) [4992]:
Using GUI port (configured interactively): 9090
Using services port (configured interactively): 9091
Using GUI initial memory (computed default, accepted): 4992
Using GUI maximum memory (computed default, accepted): 4992
Using services initial memory (computed default, accepted): 25088
Using services maximum memory (computed default, accepted): 25088
----- Part 4 of 10: SMRT View Server Setup ----
SMRT View Server requires one port (for the SMRT View GUI Webserver)
for proper operation, these ports cannot be used for listening by
any other processes. Select port numbers which do not conflict
with any other programs.
Enter the SMRT View Server (http) port [9094]:
Memory settings must be preset for SMRT View. By default, we set the
initial (-Xms) and maximum (-Xmx) Java heap sizes to the same values.
The default for SMRT View is 20% of the total memory with a maximum
of 32768 MB. We recommend using the defaults.
Pick an option:
1) raijin3.nci.org.au
2) raijin3
3) 192.43.239.23 (vlan192)
4) 10.9.105.3 (ib0)
5) Specify an alternate DNS name
Choice [1]: 1
Using dnsname (selected interactively): raijin3.nci.org.au
----- Part 3 of 10: SMRT Link Setup ----
SMRT Link requires two ports for proper operation. These ports cannot
be used for listening by any other processes. The SMRT Link GUI port
serves to redirect from an unencrypted http connection to the login
page using secure https.
Pick an option:
1) PBS
2) Other JMS
3) None (Non-Distributed Mode)
Choice [1]: 1
Using jmstype (selected interactively): PBS
Detected the following settings:
PBS_BINDIR=/opt/pbs/default/bin
PBS_QUEUE= (Use PBS default queue, currently: 'normal')
PBS_STARTARGS=
Where detected:
PBS_BINDIR (from 'PATH environment variable, default')
PBS_QUEUE (from 'default')
PBS_STARTARGS (from 'default')
#write a module file
cd ~/mymodules/
mkdir smrtlink
cd smrtlink/
vim 5.1.0
#paste this to make module
#%Module1.0#####################################################################
source /opt/Modules/extensions/extensions.tcl
proc ModulesHelp { } {
puts stderr "\tAdds smrtlink bin directory to the path"
}
module-whatis "smrtlink"
#soft-prereq python/2.7.6
#set kineticsToolsversion 1.2.1 #no version yet
prepend-path PATH /short/sd34/ap5514/myapps/smrtlink/5.1.0/install/smrtlink-release_5.1.0.26412/bundles/smrttools/smrtcmds/bin
#prepend-path PYTHONPATH /short/sd34/ap5514/myapps/kineticsTools/lib/python2.7/site-packages