intermine / ci-scripts

common intermine testmine install scripts used in multiple repos.

Warning: Not in use

These scripts have been superseded by intermine_boot. This repository is no longer being maintained.

ci-scripts

Shell scripts for setting up InterMine instances as part of CI.

Requirements

• postgresql
• openjdk8 (9 and above won't work)

To run as part of CI from another repo:

git clone https://github.com/intermine/ci-scripts
(cd ci-scripts && bash init-biotestmine.sh)

As part of a Travis pipeline:

language: java
sudo: true
jdk:
  - openjdk8
services:
  - postgresql

before_install:
    - git clone https://github.com/intermine/ci-scripts
    - (cd ci-scripts && bash init-biotestmine.sh)

If you wish to use the lighter testmodel, replace init-biotestmine.sh with init-testmine.sh.

Build biotestmine dataset from scratch

The init-biotestmine.sh script will by default restore the integrated data from a pre-built database dump. If you wish to build the dataset from scratch instead, you can specify BUILD_DATASET=true when invoking the script. Note that this will usually take upwards of 10 minutes.

Full processing of biotestmine dataset

The init-biotestmine.sh script uses a stripped down project.xml for processing the dataset. If you miss any features, you can specify NO_CONFIG_OVERRIDE=true when invoking the script to use the complete (albeit heavier) project.xml in the biotestmine repository.