AmiGO is the public interface for the Gene Ontology.
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.gitignore ignore generated data Mar 29, 2016
INSTALL.org initial pass at changes necessary for directory running Jun 19, 2014
LICENSE update Mar 26, 2015
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README.md

Overview

This README file will be filled out more in the future. However, for the time being, please see the AmiGO 2 Manual for more details about the code and installation. You may also be interested in the related information found in BBOP JS.

Installation

The main installation information is available on the wiki.

Jenkins (example)

Loading

This is a load example using this configuration.

## Get to the app home and make sure we're in the right place.
cd /home/bbop/local/src/git/amigo
git reset --hard && git pull

## Get the environment and variables ready.
npm install
cp conf/examples/amigo.yaml.tomodachi conf/amigo.yaml
## Need to generate config.pl
./node_modules/.bin/gulp install

## Do the load.
./node_modules/.bin/gulp message-load-start
/bin/rm -f /tmp/golr_timestamp.log
./node_modules/.bin/gulp golr-purge
./node_modules/.bin/gulp check-ontology-data
./node_modules/.bin/gulp load-all
./node_modules/.bin/gulp message-load-clear

Deployment & Unit Tests

This is an example automatic deployment and unit/app testing using this configuration.

## I believe Xvfb should die on shell exit?
Xvfb :1 -screen 5 1024x768x8 &

## Get to the app home and make sure we're in the right place.
cd /home/bbop/local/src/git/amigo
git pull && git reset --hard

## Get the environment and variables ready.
npm install
cp conf/examples/amigo.yaml.tomodachi conf/amigo.yaml
## Need to generate config.pl
./node_modules/.bin/gulp install

## Make the proper python virtualenv setup with the libs we need.
cd test-app/behave
virtualenv `pwd`
source bin/activate
pip install selenium behave jsonpath-rw
## Get back to top.
cd ../..

## Run unit tests against AmiGO labs (master).
DISPLAY=:1.5 ./node_modules/.bin/gulp tests

## Pop out of our wonderland.
deactivate

Releases

The SOP for releases is:

  • npm install
  • gulp release
  • cd javascript/npm/amigo2-instance-data/ && gulp release && cd ../bbop-widget-set && gulp release && cd ../../..
  • git commit -a -m "SOP update for metadata"
  • git push