Launch and manage cloud computing resources for antibody repertoire analysis
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bin fix imports and requirements for Py3 compatibility, add paramiko as a… Feb 6, 2018


EC2 instance/cluster management. Still under active development, but main commands (launch, sshmaster/sshnode, destroy, terminate, get, put) are stable and should not undergo breaking changes.


abcloud <command> <cluster_name> [options]

Launch a basic cluster named 'test' with a master and 2 workers, all m3.large:
abcloud launch test --workers 2

Launch a basic 'test' cluster with spot instance workers at a max price of $1.00/hr:
abcloud launch test --workers 2 --spot-price 1.00

SSH into the master instance of the 'test' cluster:
abcloud sshmaster test

SSH into node001 of the 'test' cluster:
abcloud sshnode test --node node001

Put a file (local path: '~/myfile') onto the master instance of the 'test' cluster (remote path: '/scratch'):
abcloud put test ~/myfile /scratch

Put the same file onto node001 of the 'test' cluster:
abcloud put test --node node001 /home/me/myfile /scratch

Terminate the 'test' cluster:
abcloud terminate test

Destroy the 'test' cluster (same as terminate, but also deletes security groups):
abcloud destroy test

Launch a single instance (r3.2xlarge) named 'jupyter' running a Jupyter Notebook server:
abcloud launch jupyter --instance-type r3.2xlarge --jupyter

Launch 'jupyter' instance running a Jupyter server, but using spot pricing:
abcloud launch jupyter --jupyter --spot-price 2.00 --force-spot-master

Launch a single instance named 'mongo' running MongoDB with 8x500GB EBS volumes in RAID10:
abcloud launch mongo --master-ebs-vol-num 8 --master-ebs-vol-size 500 --master-ebs-raid-level 10 --mongodb

To get a full list of options and default settings:
abcloud --help


Python 2.7 (3.x probably doesn't work, but hasn't been tested)

All of the above dependencies can be installed with pip. If you're new to Python, a great way to get started is to install the Anaconda Python distribution (, which includes pip as well as a ton of useful scientific Python packages.