KBaseFBAModeling

This is the repository for the KBase module containing the web services for FBA modeling in KBase.

Development Deployment

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

This module depends upon the following KBase modules:

kb_model_seed
kb_seed
idserver
workspace_service
auth

And the following services / software:

Running IDServer
Running workspace_service
GLPK ( run which glpsol to see if you have it)

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 kbase@git.kbase.us:dev_container.git
cd ~/dev_container
./bootstrap /kb/runtime
source user-env.sh
cd modules
git clone kbase@git.kbase.us:KBaseFBAModeling.git

Setup Services

To deploy a test version (with test data):

cd ~/dev_container/modules
git clone kbase@git.kbase.us:kb_model_seed.git
git clone kbase@git.kbase.us: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