AmiGO2 install

GOLR install:

There are a few prerequisites to getting GOLR installed. They appear to be Maven and OwlTools. To install maven, I followed the instructions from here: http://blog.gluster.org/2013/08/yum-install-maven-yes-you-can/, seemed to work without error.

Then, to install OWLTools, I did the following:

cd /lemma/justin

svn co http://owltools.googlecode.com/svn/trunk/ owltools

This creates the owltools directory in my space on lemma.

To compile OWLTools, run:

mvn clean package

This will take about half an hour.

Grab the 3.6 version of SOLR from apache and unpack:

wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz

tar zxvf apache-solr-3.6.2.tgz

Pull down the latest version of AmiGO:

cd /data/www/planteome_dev

git clone https://github.com/geneontology/amigo.git amigo

Go back to the SOLR directory and replace the config with those from GOLR:

cd /lemma/justin/SOLR/apache-solr-3.6.2/example/solr/conf

cp schema.xml schema.xml.org

cp solrconfig.xml solrconfig.xml.org

cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):

cd ../../ (be in the example directory)

java -jar start.jar

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined on this page

Had to modify that script as follows to make it work on CentOS:

elserj@palea init.d]$ diff solr solr.org 
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
< 
24c20
<     daemon "cd /data/www/planteome_dev/SOLR/example; java -jar start.jar &> /var/log/solr/solr.log &"
---
>     daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
<     ps -aef | grep start.jar | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
>     daemon --stop --name=solr  --verbose

This page will be updated as I progress.