Assembly Service

Overview

This is a service to assemble genomes and metagenomes with user's choice of assembly software. It currently supports more than 20 assemblers and processing modules.

REST API

Deploying only the client

Toolchain:

• make
• git

Interpreters:

• Python 2.7.x (with SSL support)
• Perl 5

Python packages (with pip):

• appdirs
• argparse
• httplib2
• pkg_resources
• prettytable
• requests
• setuptools
• ssl (built in)

Perl modules (with CPAN http://perl.about.com/od/packagesmodules/qt/perlcpan.htm):

• Config/Simple.pm
• DateTime.pm
• JSON.pm
• HTTP/Request.pm
• LWP/UserAgent.pm
• Term/ReadKey.pm
• Text/Table.pm

git clone https://github.com/kbase/assembly.git
cd assembly
make -f Makefile.standalone

Deploying and Testing AssemblyRAST 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://kbase@git.kbase.us/dev_container
cd /kb/dev_container
./bootstrap /kb/runtime
source user-env.sh
cd /kb/dev_container/modules
git clone ssh://kbase@git.kbase.us/assembly
git fetch origin
git checkout RC
make deploy
make test

Deploying AssemblyRAST 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://kbase@git.kbase.us/dev_container
cd /kb/dev_container/modules
git clone ssh://kbase@git.kbase.us/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 compute server
• for now, we assume a long-running compute 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 service listen on port 5672, so this port must be open
• after starting the service, the process id of the service 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