Difference between revisions of "SeqShop: Calling Your Own Genome, December 2014"
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== Setup == | == Setup == |
Revision as of 17:57, 6 December 2014
Login instructions for seqshop-server
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
- 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.
- Open putty
- Start->Enter "putty" in the search and select "PuTTY" from the program list
- Configure PuTTY in the PuTTY Configuration window
- Host Name:
seqshop-server.sph.umich.edu
- 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
- 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/setup.2x.txt export SAMPLE=Sample_XXXXX export ALIGN_OUT=~/personal/output export CHR20_OUT=~/personal/output.20 mkdir -p $CHR20_OUT export EXOME_OUT=~/personal/output.exome mkdir -p $EXOME_OUT
ALIGN_OUT needs to point to where your alignment output went, so if your output is not ~/personal/output, please set OUT appropriately
Verify that this does not give an error:
ls $ALIGN_OUT/bams/${SAMPLE}.recal.bam
Chromosome 20
We want to add the 100 1000G chr20 BAMs to your bam list. Let's copy the original one into a new one so we can run other tests later.
cp $ALIGN_OUT/bam.index $CHR20_OUT/bam.20.index
Now add the chr20 BAMs to your new bam list:
cat $IN/chr20/bam.20.index >> $CHR20_OUT/bam.20.index
We are going to run on the cluster, so edit the first line of $CHR20_OUT/bam.20.index to give the cluster path to your info file.
nedit $CHR20_OUT/bam.20.index
Replace the /home on the first line with /net/seqshop-server
Verify you have 101 lines in your list:
wc -l $CHR20_OUT/bam.20.index
Update your gotcloud configuration file to indicate only chromosome 20 and point to the new list:
nedit ~/personal/gotcloud.2x.conf
Replace all occurrances of /home with /net/seqshop-server - this will allow you to access your home directory from jobs running on the mini-cluster
Update OUT_DIR & BAM_INDEX to:
OUT_DIR = $(IN_DIR)/output.20 BAM_INDEX = $(OUT_DIR)/bam.20.index
Tell it you only want to process chromosome 20, by adding the following anywhere in the file:
CHRS = 20
Since it would take a while to run chrom 20 for 101 samples, I already ran the first step for the 100 1000G samples.
We will "trick" GotCloud into thinking you already ran them by copying them into your output directory.
cp -r $IN/chr20/glfs $CHR20_OUT/.
Now you are ready to run. Specify your chr20 bam list on the command line (or you could update BAM_INDEX in your conf file.
Run 4 jobs on our mini-cluster
$GC/gotcloud snpcall --conf ~/personal/gotcloud.2x.conf --numjobs 4 --batchtype mosix --batchopts "-j10,11,12,13"
- --batchtype says to use mosix (our cluster system)
- --batchopts tells mosix the options to run with
- for mosix, -j10,11,12,13 says to run on nodes 10, 11, 12, & 13 - the names of the 4 nodes on our mini-cluster
Exome
To speed things up, I extracted only exome regions from 100 1000g low coverage BAMs.
Let's create a new bam info file with your BAM combined with those BAMs.
cp $ALIGN_OUT/bam.index $EXOME_OUT/bam.exome.index
Now add the exome BAMs to your new bam list:
cat $IN/exome/bam.exome.index >> $EXOME_OUT/bam.exome.index
Verify you have 101 lines in your list:
wc -l $EXOME_OUT/bam.exome.index
We are going to run on the cluster, so edit the first line of $EXOME_OUT/bam.exome.index to give the cluster path to your info file.
nedit $EXOME_OUT/bam.exome.index
Replace the /home on the first line with /net/seqshop-server
Locate your gotcloud.2x.conf (probably at: ~/personal/gotcloud.2x.conf) and open it in your favorite editor:
nedit ~/personal/gotcloud.2x.conf
Replace all occurrances of
/home with /net/seqshop-server
This is so you can run on the mini-cluster we have and can run more jobs at once
Update OUT_DIR & BAM_INDEX to:
OUT_DIR = $(IN_DIR)/output.exome BAM_INDEX = $(OUT_DIR)/bam.exome.index
Update your gotcloud configuration file to indicate exomes:
# 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
Remove CHRS = 20
Since it would take a while to run all 101 samples, I already ran the first step for the 100 1000G samples. We will "trick" GotCloud into thinking you already ran them by copying them into your output directory.
cp -r $IN/exome/glfs $EXOME_OUT/.
Run 4 jobs on our mini-cluster
$GC/gotcloud snpcall --conf ~/personal/gotcloud.2x.conf --numjobs 4 --batchtype mosix --batchopts "-j10,11,12,13"
- --batchtype says to use mosix (our cluster system)
- --batchopts tells mosix the options to run with
- for mosix, -j10,11,12,13 says to run on nodes 10, 11, 12, & 13 - the names of the 4 nodes on our mini-cluster