kbaseattic / amethst_service

AMETHST, or Analysis METHod Selection Tool, is an automated pipeline that makes it possible to objectively assess the relative performance of multiple analysis methods applied to annotation abundance data. Utilizing objective, permutation-based statistics, it can determine the best performing analysis from any arbitrary collection of analyses, and can also determine the degree to which each analysis step (e.g. normalization and reprocessing of the data, selection of distance/dissimilarity metric) affects the results produced by each analysis method.

amethst service

AMETHST, or Analysis METHod Selection Tool, is an automated pipeline that makes it possible to objectively assess the relative performance of multiple analysis methods applied to annotation abundance data. Utilizing objective, permutation-based statistics, it can determine the best performing analysis from any arbitrary collection of analyses, and can also determine the degree to which each analysis step (e.g. normalization and reprocessing of the data, selection of distance/dissimilarity metric) affects the results produced by each analysis method.

Deployment in KBase

configure deploy.cfg

make

one of:

make deploy-client
make deploy-service
make deploy-backend
make deploy-all

then

source /kb/deployment/user-env.sh

one of

make test-client
make test-service
make test-backend
make test

Creating a backend compute VM

Script location (the script is located in the AMETHST repository linked to this amethst_service repository):

AMETHST/installation/Install_AMETHST_compute_node.havannah.sh

Script should be executed with envrionment variables that include KB_AUTH_TOKEN and AWE_CLIENT_GROUP_TOKEN:

sudo -E Install_AMETHST_compute_node.havannah.sh

Instructions to install amethst client script independently

USAGEPOD library

wget https://raw.githubusercontent.com/wgerlach/USAGEPOD/master/lib/USAGEPOD.pm

SHOCK client library

mkdir SHOCK
cd SHOCK
wget https://raw.githubusercontent.com/MG-RAST/Shock/master/libs/SHOCK/Client.pm
cd ..

amethst client script

wget https://raw.githubusercontent.com/kbase/amethst_service/master/plbin/mg-amethst.pl
chmod +x mg-amethst.pl

configuration to use KBase amethst service

export SHOCK_SERVER_URL=
export KB_AUTH_TOKEN=<your kbase token>

The token can also be passed with --token= to mg-amethst.pl