95d69c9ca4a828e7d95f7adc759f517e8228cd1a
AWS.md
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1 | +## SBGrid in AWS EC2 |
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2 | + |
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3 | +### Compatible AMIs |
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4 | +``` |
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5 | + __| __|_ ) |
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6 | + _| ( / Amazon Linux AMI |
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7 | + ___|\___|___| |
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8 | +``` |
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9 | +We recommend CentOS / RHEL 7 AMIs for the SBGrid software stack. |
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10 | +Amazon AMIs appear to work as well. |
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11 | +Debian / Ubuntu AMIs may work but are untested. |
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12 | +If you have problems let us know. |
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13 | + |
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14 | +### Prerequisites |
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15 | + |
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16 | +First install tcsh since it is not typically provided but is required by several titles. |
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17 | + |
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18 | + sudo yum install tcsh |
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19 | + |
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20 | +### Download the SBGrid command line interface |
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21 | +First, login to your instance and download the SBGrid CLI install client. |
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22 | + |
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23 | +``` |
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24 | +curl -LO https://sbgrid.org/wiki/downloads/sbgrid-1.0.694-Linux.tgz |
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25 | +tar -zxvf sbgrid-1.0.694-Linux.tgz |
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26 | +cd sbgrid-1.0.694-Linux |
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27 | +``` |
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28 | + |
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29 | +### Activate your installation |
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30 | +If you don't have a username and key, register here : [https://sbgrid.org/registration/register/](https://sbgrid.org/registration/register/) |
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31 | + |
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32 | +``` |
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33 | +./sbgrid activate <site> <user> <key> |
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34 | +``` |
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35 | + |
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36 | +### Install programs |
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37 | + |
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38 | +EPMR as an example here - |
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39 | + |
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40 | +``` |
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41 | +./sbgrid install epmr |
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42 | +``` |
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43 | + |
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44 | +### Run your software |
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45 | +Initialize the environment, and the instance is ready to go. |
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46 | + |
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47 | +``` |
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48 | +source /programs/sbgrid.shrc |
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49 | +``` |
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50 | + |
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51 | + |
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52 | +``` |
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53 | +[ec2-user@ip-172-31-62-107 sbgrid-1.0.694-Linux]$ source /programs/sbgrid.shrc |
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54 | +******************************************************************************** |
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55 | + Software Support by SBGrid (www.sbgrid.org) |
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56 | +******************************************************************************** |
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57 | + SBGrid Announcements |
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58 | + - OpenMPI has been updated. RELION users please see |
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59 | + <https://sbgrid.org/software/titles/relion> for mpirun version info. |
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60 | +******************************************************************************** |
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61 | + Your use of the applications contained in the /programs directory constitutes |
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62 | + acceptance of the terms of the SBGrid License Agreement included in the file |
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63 | + /programs/share/LICENSE. The applications distributed by SBGrid are licensed |
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64 | + exclusively to member laboratories of the SBGrid Consortium. |
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65 | +******************************************************************************** |
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66 | + SBGrid was developed with support from its members, Harvard Medical School, |
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67 | + HHMI, and NSF. If use of SBGrid compiled software was an important element |
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68 | + in your publication, please include the following reference in your work: |
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69 | + |
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70 | + Software used in the project was installed and configured by SBGrid. |
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71 | + cite: eLife 2013;2:e01456, Collaboration gets the most out of software. |
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72 | +******************************************************************************** |
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73 | + SBGrid installation last updated: 2018-05-24 |
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74 | + Please submit bug reports and help requests to: <bugs@sbgrid.org> or |
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75 | + <http://sbgrid.org/bugs> |
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76 | +******************************************************************************** |
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77 | + Capsule Status: Active |
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78 | + For additional information visit https://sbgrid.org/wiki/capsules |
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79 | +******************************************************************************** |
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80 | +``` |
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81 | + |
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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) |
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33 | 34 | |
34 | 35 | Portals |
35 | 36 | * [Data Processing After WSMR](wsmr-worked) |