leereilly / assembly

An extensible framework for genome assembly.

Assembly Services

Overview

Service to assemble genomes and metagenomes with user's choice of assembly algorithm. Currently supports more than 20 assemblers and processing modules. More to come...

Deploying and Testing AssembyRAST client on KBase infrastructure

• start with a fresh KBase image (last tested on v15) with security group 'default' or 'assembly-rast-group'
• log in as ubuntu and get root access with 'sudo su'
• enter the following commands:

cd /kb
git clone ssh://[email protected]/dev_container
cd /kb/dev_container
./bootstrap /kb/runtime
source user-env.sh
cd /kb/dev_container/modules
git clone ssh://[email protected]/assembly
git fetch origin
git checkout RC
make deploy
make test

Deploying AssembyRAST server on KBase infrastructure

• start with a fresh KBase image (last tested on v14) with security group 'assembly-rast-group'
• log in as ubuntu and get root access with sudo su
• enter the following commands:

cd /kb
git clone ssh://[email protected]/dev_container
cd /kb/dev_container/modules
git clone ssh://[email protected]/assembly
cd /kb/dev_container
./bootstrap /kb/runtime
source user-env.sh
make deploy-service

Dependencies

The current deployment first invokes scripts/install_dependencies.sh. This will be no longer necessary once a kbase image is built with these dependencies.

Starting/Stopping the service

• the assembly service includes one control server and at least one computer server
• for now, we assume a long-running computer server, and use 'service' to refer to the control server
• to start and stop the service, use the 'start_service' and 'stop_service' scripts in /kb/deployment/services/assemly
• on test machines, assembly services listen on port 5672, so this port must be open
• after starting the service, the process id of the serivice is stored in the 'service.pid' file in /kb/deployment/services/assembly/

TODO

Client deployment Testing Support for more assemblers Support for large eukaryotic genome assembly Support for metagenome assembly on supercomputer ...