SeqShop: Calling Your Own Genome, June 2014

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Revision as of 18:51, 19 June 2014 by Mktrost (talk | contribs) (→‎Run)
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Login to the seqshop-server Linux Machine

This section will appear redundantly in each session. If you are already logged in or know how to log in to the server, please skip this section

  1. Login to the windows machine
  • The username/password for the Windows machine should be written on the right-hand monitor
  • Start xming so you can open external windows on our Linux machine
    • Start->Enter "Xming" in the search and select "Xming" from the program list
    • Nothing will happen, but Xming was started.
    • View Screenshot

      • Xming.png

  • Open putty
    • Start->Enter "putty" in the search and select "PuTTY" from the program list
    • View Screenshot

      • PuttyS.png

  • Configure PuTTY in the PuTTY Configuration window
    • Host Name: seqshop-server.sph.umich.edu
    • View Screenshot

      • Seqshop.png

    • Setup to allow you to open external windows:
      • In the left pannel: Connection->SSH->X11
        • Add a check mark in the box next to Enable X11 forwarding
        • View Screenshot

          • SeqshopX11.png

    • Click Open
    • If it prompts about a key, click OK
  • Enter your provided username & password as provided


    • You should now be logged into a terminal on the seqshop-server and be able to access the test files.

    • If you need another terminal, repeat from step 3.

    Login to the seqshop Machine

    So you can each run multiple jobs at once, we will have you run on 4 different machines within our seqshop setup.

    • You can only access these machines after logging onto seqshop-server

    3 users logon to: 

    ssh -X seqshop1

    3 users logon to: 

    ssh -X seqshop2

    2 users logon to: 

    ssh -X seqshop3

    2 users logon to: 

    ssh -X seqshop4

    Setup

    Set these values. If you used a different path for any of these, please update here. Also, be sure to specify your sample name instead of Sample_XXXXX 

    source /home/mktrost/seqshop-server/setup.txt
export SAMPLE=Sample_XXXXX

    OUT needs to point to where your alignment output went, so if your output is not ~/personal/output, please set OUT appropriately: 

    export OUT=~/personal/YOUR_OUTPUT_DIR

    Verify that this does not give an error: 

    ls $OUT/bams/${SAMPLE}.recal.bam

    GotCloud Configuration Updates

    To speed things up, we will only run on certain regions

    • We need to update the GotCloud Configuration to do this.

    Locate your gotcloud.2x.conf (probably at: ~/personal/gotcloud.2x.conf) and open it in your favorite editor: 

    nedit  ~/personal/gotcloud.2x.conf

    Add 

    # Specify the path to the regions we want to call
UNIFORM_TARGET_BED = $(REF_DIR)/20130108.exome.targets.nochr.bed

# We do not want any off target bases
OFFSET_OFF_TARGET = 0

WRITE_TARGET_LOCI = TRUE
TARGET_DIR = target

    Run

    Set CHR = 1 2

    cp -r /home/mktrost/seqshop/inputs/glfs personal/output/.

    cp personal/output/bam.index personal/output/bam.exome.index

    cat /home/mktrost/seqshop/inputs/20130502.gotcloud.low_coverage.100.index >> personal/output/bam.exome.index

    wc -l personal/output/bam.exome.index

    cp /home/mktrost/seqshop/inputs/gotcloud.exome.conf personal/.

    Update the conf ...your home.

    /home/mktrost/seqshop/gotcloud/gotcloud snpcall --conf personal/gotcloud.exome.conf

    Retrieved from "http://genome.sph.umich.edu/w/index.php?title=SeqShop:_Calling_Your_Own_Genome,_June_2014&oldid=11029"