assembly

Created: 2014-05-19 19:38
Updated: 2019-01-11 02:37
License: mit

README.md

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
Cookies help us deliver our services. By using our services, you agree to our use of cookies Learn more