Follow the step-by-step tutorial below to run Juicer on AWS. If you have any questions at all, please do not hesitate to contact us!
Disclaimer: Running EC2 has a cost by the hour - as long as the instance is running, you will be charged. Please make sure you understand Amazon's pricing policies before you start working with AWS.
This file will act as a password of sorts, and should be saved in a secure location on your computer.
Note: get the public IP address from the View Instances page (50.16.4.165 in the example here).
cd /path/to/folderUpdate the permissions for the private key.
chmod 600 juicer_aws.pemConnect with the AWS instance (ssh via public IP).
ssh -i juicer_aws.pem [email protected]
Do not select "Generate a public/private key pair".
A pop-up will appear saying you have imported a key. You'll then have the option to Save private key. Save it without a passphrase as juicer_aws.ppk.This is different from your public IP address
.
/sbin/ifconfig | grep "inet addr" | awk -F: '{print $2}' | awk '{print $1}' |head -1Now change the last line in the hosts file to list the internal IP address
sudo vim /etc/hostsThen set the hostname and restart the services
sudo hostname HEADNODE sudo service openlava restart sudo /etc/init.d/networking restartYou should also update your password (default is aidenlab2015)
sudo passwd ubuntuBefore running Juicer for the first time, you should also update to the lastest scripts from Github by running the following
cd ~ wget https://github.com/theaidenlab/juicer/archive/master.zip unzip master.zip sudo cp -TR juicer-master/AWS/scripts /opt/juicer/scripts
cd /opt/juicer/workCreate a new directory for each experiment. Also create a fastq folder in each experiment's directory.
mkdir -p EXP1/fastqCopy all your fastq files into the appropriate fastq folder (e.g.
/opt/juicer/work/EXP1/fastq
).cd /opt/juicer/work/EXP1/And issue the juicer command (default assumes -g hg19 -s MboI)
/opt/juicer/scripts/juicer.shWait for script to finish. Once all jobs have been submitted, you can check on their status
bjobsLSF will eventually report
No unfinished job foundThe output file (e.g.
/opt/juicer/work/EXP1/lsf.out
) should end with the line
Pipeline successfully completedResults will be available in the aligned folder under your work directory (e.g.
/opt/juicer/work/EXP1/aligned
).Juicer is currently in its alpha release. For general questions, please use the forum. If you have further difficulties using Juicer, please do not hesitate to contact us.
If you use Juicer in your research, please cite:
Neva C. Durand*, Muhammad S. Shamim*, Ido Machol, Suhas S. P. Rao, Miriam H. Huntley, Eric S. Lander, and Erez Lieberman Aiden. "Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments." Cell Systems (In Press).
Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. "A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping." Cell 159, 2014.
* contributed equally