AWS.md
... ...
@@ -0,0 +1,82 @@
1
+## SBGrid in AWS EC2
2
+
3
+### Compatible AMIs
4
+```
5
+ __| __|_ )
6
+ _| ( / Amazon Linux AMI
7
+ ___|\___|___|
8
+```
9
+We recommend CentOS / RHEL 7 AMIs for the SBGrid software stack.
10
+Amazon AMIs appear to work as well.
11
+Debian / Ubuntu AMIs may work but are untested.
12
+If you have problems let us know.
13
+
14
+### Prerequisites
15
+
16
+First install tcsh since it is not typically provided but is required by several titles.
17
+
18
+ sudo yum install tcsh
19
+
20
+### Download the SBGrid command line interface
21
+First, login to your instance and download the SBGrid CLI install client.
22
+
23
+```
24
+curl -LO https://sbgrid.org/wiki/downloads/sbgrid-1.0.694-Linux.tgz
25
+tar -zxvf sbgrid-1.0.694-Linux.tgz
26
+cd sbgrid-1.0.694-Linux
27
+```
28
+
29
+### Activate your installation
30
+If you don't have a username and key, register here : [https://sbgrid.org/registration/register/](https://sbgrid.org/registration/register/)
31
+
32
+```
33
+./sbgrid activate <site> <user> <key>
34
+```
35
+
36
+### Install programs
37
+
38
+EPMR as an example here -
39
+
40
+```
41
+./sbgrid install epmr
42
+```
43
+
44
+### Run your software
45
+Initialize the environment, and the instance is ready to go.
46
+
47
+```
48
+source /programs/sbgrid.shrc
49
+```
50
+
51
+
52
+```
53
+[ec2-user@ip-172-31-62-107 sbgrid-1.0.694-Linux]$ source /programs/sbgrid.shrc
54
+********************************************************************************
55
+ Software Support by SBGrid (www.sbgrid.org)
56
+********************************************************************************
57
+ SBGrid Announcements
58
+ - OpenMPI has been updated. RELION users please see
59
+ <https://sbgrid.org/software/titles/relion> for mpirun version info.
60
+********************************************************************************
61
+ Your use of the applications contained in the /programs directory constitutes
62
+ acceptance of the terms of the SBGrid License Agreement included in the file
63
+ /programs/share/LICENSE. The applications distributed by SBGrid are licensed
64
+ exclusively to member laboratories of the SBGrid Consortium.
65
+********************************************************************************
66
+ SBGrid was developed with support from its members, Harvard Medical School,
67
+ HHMI, and NSF. If use of SBGrid compiled software was an important element
68
+ in your publication, please include the following reference in your work:
69
+
70
+ Software used in the project was installed and configured by SBGrid.
71
+ cite: eLife 2013;2:e01456, Collaboration gets the most out of software.
72
+********************************************************************************
73
+ SBGrid installation last updated: 2018-05-24
74
+ Please submit bug reports and help requests to: <bugs@sbgrid.org> or
75
+ <http://sbgrid.org/bugs>
76
+********************************************************************************
77
+ Capsule Status: Active
78
+ For additional information visit https://sbgrid.org/wiki/capsules
79
+********************************************************************************
80
+```
81
+
82
+If you have problems let use know - bugs@sbgrid.org
_Sidebar.md
... ...
@@ -30,6 +30,7 @@ Hardware Support Notes
30 30
* [Recommended Hardware](recommended)
31 31
* [GPU computing](gpu)
32 32
* [Setup Stereo 3D](stereo)
33
+# [SBGrid on AWS EC2](AWS)
33 34
34 35
Portals
35 36
* [Data Processing After WSMR](wsmr-worked)