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Revision as of 20:43, 10 December 2014
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''Login instructions for seqshop-server''
''Login instructions for seqshop-server''
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== Wednesday ==
== Wednesday ==
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diff $SAMPLE/gotcloud.conf ~mktrost/NA12878/gotcloud.conf
diff $SAMPLE/gotcloud.conf ~mktrost/NA12878/gotcloud.conf
'''If you see differences, you can modify your file using nedit (or your favorite editor as you used yesterday).'''
'''If you see differences other than OUT_DIR, you can modify your file using nedit (or your favorite editor as you used yesterday).'''
* '''Or you can copy my file and just change OUT_DIR:'''
* '''Or you can copy my file and just change OUT_DIR:'''
cp ~mktrost/NA12878/gotcloud.conf $SAMPLE/gotcloud.conf
cp ~mktrost/NA12878/gotcloud.conf $SAMPLE/gotcloud.conf
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== Thursday ==
== Thursday ==
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Detach from screen. We will resume it again later when we restart SNPCall (if necessary).
Detach from screen. We will resume it again later when we restart SNPCall (if necessary).
Ctrl-a d
Ctrl-a d
We will Resume SNP Calling (if necessary) after the practical.
We will Resume SNP Calling (if necessary) after the practical.
=== Restart SnpCall ===
==== Resume screen ====
;How do you log back into screen?
screen -r
This will resume an already running screen.
Your screen session still has your environment variables set, so you do not need to reset them.
==== Running SnpCall ====
Run GotCloud snpcall with 6 jobs running in parallel
${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 6
* GotCloud will pick up after the last completed step from before.
This will run overnight. We will check if it completed at the practical in the morning.
==== Log Out ====
;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.
exit PuTTY
=== Thursday FEEDBACK! ===
Please provide feedback on the lectures/tutorials from today:
