Skip to content

Server to support authentication and retrieval of genomes from the SEED environment

Notifications You must be signed in to change notification settings

ModelSEED/MSSeedSupportServer

Repository files navigation

MSSeedSupportServer

This is a repository to support authentication and retrieval of genomes from the SEED environment.

Development Deployment

NOTE: deploy on a server with at least 8 gb RAM

This module depends upon the following KBase modules:

  • kb_model_seed

And the following services / software:

  • Running IDServer

The setup commands should be run as root to allow for creation and editing of base level directories.

Checkout a dev_container and run the bootstrap script in the container. Source the resulting user-env.sh script. Checkout this repository into the modules directory.

cd ~
git clone [email protected]:dev_container.git
cd ~/dev_container
./bootstrap /kb/runtime
source user-env.sh
cd modules
git clone [email protected]:KBaseFBAModeling.git 

Setup Services

To deploy a test version (with test data):

cd ~/dev_container/modules
git clone [email protected]:kb_model_seed.git
git clone [email protected]:idserver.git
cd ..
./bootstrap /kb/runtime
source user-env.sh
make
make deploy

The make and make deploy scripts may complain about missing modules. However the deploy will automatically download and install those missing modules.

Setup Test-Data

Note: requires a local MongoDB

export PATH=$PATH:/kb/deployment/bin
export PERL5LIB=$PERL5LIB:/kb/deployment/lib/perl5
ms createuser kbase   # use the password 'kbase' when prompted
ms login kbase        # use the password 'kbase' when prompted
ms stores add mongo --type mongo --host localhost
ms import biochemistry default
ms import mapping default -b default

Start Service

Note: copy the contents of deploy.cfg into /kb/deployment/deployment.cfg

cd /kb/deployment/services/fbaModelServices
./start_service

Note: check /kb/deployment/services/fbaModelServices/error.log to verify the service is running properly

Testing

server-tests: see configs/test.cfg for default settings for server-tests client-tests: configured to run against a workspace service on the localhost. Either change to the production workspace service, or restart the fbaModelService on localhost with local workspace service (see /kb/deployment/deployment.cfg).

About

Server to support authentication and retrieval of genomes from the SEED environment

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published