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title: UPPMAX Tutorial Q&A

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# UPPMAX Tutorial Q&A

**How do i get help?**
Either write your question here or write which breakout room you need help in. Or just drop out of the breakout room back to the main room and ask for help.





## do we meet again in the afternoon or we just do the tutorials by ourselves?
There is no more lecture so feel free to continue on your own if you want. I will be in the zoom room and here to answer question until 17:00.

## how do i quit viewing the data.bam? I am using the terminal on mac
Press q or ctrl+c a couple of times.
great!

## Where is the "exome_analysis_script.sh" shell script file in pipeline tutorial? We tried following the tutorial and it appears that the file "exome_analysis_script.sh" is missing and we cannot follow the rest of the tutorial without it. It appears that we followed the copying from the "/sw/courses/ngsintro/linux/uppmax_pipeline_exercise/data/" properly as other directories and files are here.
ok, there is none yet. you will created it yourself. When you type 'nano exome_analysis_scipt.sh', if it does not exist it will be created. 

-- Hi, we can create the file but are you expecting us to call the functions and directory as they are the pictures?

No, the picture is probably wrong when it comes to project ids and such. The commands in general should be valid though.

-- But I think we do not know enough functions within these programs/tools to make a script maybe. That we can try perhaps. But we might make mistakes in calling the directories and affecting the main files. 

-- I think the commands you should have in the scrip are the same as when you ran them manually in the terminal.

-- Yes, we can run the commands manually before putting them in a script but are they available somewhere or we are expected to write them on our own?

-- as long as you do the export PATH=.... thing inside the script as well, it should work just as in the terminal. There is no file like the one in the image. You have to write it yourself. It is an image to prevent copy/pasting :)

-- Alright! Thank you! We will try.

-- So, sh script worked and the sbatch script job is in queue.


UPPMAX is terribly slow when changing directories today!



yeah... when the file systems are this full they get slower. :/

I have problems running diff_exp in a script but it works on the command line
Oh it works but the input files has to have ext .sam I think

let's see. Yes, it seems like it has to be a .sam file you use as input.


Ok. Thanks for a great tutorial. Have a nice weekend!

Thanks for taking it! have a nice weekend you too!



