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, 01:33, 18 June 2014
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| You'll notice that this file is very similar to the one we have been using. | | You'll notice that this file is very similar to the one we have been using. |
| * Just a few modifications to run a new test on the whole genome | | * Just a few modifications to run a new test on the whole genome |
| + | |
| + | == Run your Alignment == |
| + | |
| + | === Screen === |
| + | The alignment pipeline will run overnight, but you'll want to log out. |
| + | |
| + | ; How do I leave something running on the server even if I log out? |
| + | : One solution is screen! |
| + | |
| + | ; How do I use screen? |
| + | : Before running your command, you need to start screen: |
| + | : <pre>screen</pre> |
| + | |
| + | [[File:Screen.png]] |
| + | |
| + | As it says, press <code>Space</code> or <code>Return</code>. |
| + | * It should now look basically the same as your normal command line. |
| + | |
| + | You can now start your alignment: |
| + | /home/mktrost/seqshop/gotcloud/gotcloud align --conf ~/personal/gotcloud.2x.conf --numjobs 1 |
| + | Yes, leave that as /home/mktrost/seqshop/gotcloud/gotcloud - that is where gotcloud is installed. The ~/... points GotCloud to your specific configuration file. |
| + | |
| + | You should now see your alignment running: |
| + | |
| + | ;Want to log out and leave your job running? |
| + | In the screen window, type: |
| + | Ctrl-a d |
| + | (Hold down Ctrl and type 'a', let go of both and type 'd') |
| + | * This will "detach" from your screen session while your alignment continues to run. |
| + | |
| + | ;How do you log back into screen tomorrow? |
| + | screen -r |
| + | This will resume an already running screen. |
| + | * Feel free to test it out and you will see your alignment still running |
| + | ** Just use Ctrl-a d to detach from screen and leave your job running |