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