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

kbaseattic / assembly

readme