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Revision as of 01:33, 18 June 2014
, 01:33, 18 June 2014→Create your GotCloud Configuration File
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
