AmiGO2 install: Difference between revisions

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== GOLR 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.
Install the 3.6 version of SOLR
 
===OWLTools===
Then, to install OWLTools, I did the following:
<pre>
cd /lemma/justin
svn co http://owltools.googlecode.com/svn/trunk/ owltools
</pre>
This creates the owltools directory in my space on lemma.
 
 
To compile OWLTools, run:
<pre>
cd OWLTools-Parent
mvn clean package
</pre>
This will take about half an hour.


===SOLR===
===SOLR===
Line 54: Line 38:
Had to modify that script as follows to make it work on CentOS:
Had to modify that script as follows to make it work on CentOS:


<pre>elserj@palea init.d]$ diff solr solr.org  
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org  
16,19d15
16,19d15
< # Source function library.
< # Source function library.
Line 61: Line 45:
<  
<  
24c20
24c20
<    daemon "cd /data/www/planteome_dev/SOLR/example; java -jar start.jar &> /var/log/solr/solr.log &"
<    daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/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
>    daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
40c36
<    ps -aef | grep start.jar | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
<    ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
---
>    daemon --stop --name=solr  --verbose</pre>
>    daemon --stop --name=solr  --verbose


At this point, SOLR is now running.  Next is to load data to it.
At this point, SOLR is now running.  Next is to load data to it.
==Load data into GOLR instance==
First we need to pull down the latest AmiGO code from git:
<pre>cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>
In the <i>metadata</i> folder are the yaml files that tell owltools how to populate the fields in GOLR
Edit the golr/Makefile to fit our server:
<pre>[elserj@palea golr]$ diff Makefile Makefile.org
18c18
< MAVEN_EXE ?= /usr/bin/mvn
---
> MAVEN_EXE ?= ~/local/src/java/apache-maven-3.0.4/bin/mvn
21c21
< SOLR_URL ?= http://dev.planteome.org:8983/solr
---
> SOLR_URL ?= http://localhost:8080/solr/
24,27c24,27
< OWLTOOLS_ROOT ?= /nfs0/BPP/Jaiswal_Lab/justin/owltools/
< BBOP_JS_ROOT ?= /data/www/planteome_dev/amigo/external/
< #PANTHER_FILES_DIR ?= ~/local/src/svn/geneontology.org/trunk/experimental/trees/panther_data/
< #SOLR_DATA_ROOT ?= /srv/solr
---
> OWLTOOLS_ROOT ?= ~/local/src/git/owltools/
> BBOP_JS_ROOT ?= ~/local/src/git/bbop-js/
> PANTHER_FILES_DIR ?= ~/local/src/svn/geneontology.org/trunk/experimental/trees/panther_data/
> SOLR_DATA_ROOT ?= /srv/solr</pre>
===load-ontology===
Try to run the load-ontology part of the Makefile:
<pre>make load-ontology</pre>
This will take some time as it appears to be updating the owltools and then loading the ontologies
At this point, I get an error when trying to load the ontologies.  Working with Seth to figure it out.
Errors were mostly caused by memory issues.  Had to comment out the ncbitaxon.owl ontology from the list of ones ran.  Upped the memory to 20GB on palea.  May eventually have to look at running the load on one of the cluster nodes as they have much more RAM.  Would have to figure out how to open up the SOLR port to the internal network though.
Now to get annotation test data into GOLR
<pre>make load-test-gaf</pre>
This took a few minutes to run, not long.
At this point, data for an initial test is loaded into SOLR, next is to get AmiGO2 up and running off that instance.


==AmiGO2 install==
==AmiGO2 install==
Since we already have pulled the amigo code from git, we have to work on configuring it:
Copy the example amigo.yaml file and make the following changes:
 
<pre>  
<pre>cd amigo/conf
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
cp .initial_values.yaml amigo.yaml
</pre>
 
Change the amigo.yaml file as follows:
<pre>[elserj@palea conf]$ diff amigo.yaml .initial_values.yaml
5c5
5c5
<  value: http://planteome.org/amigo/cgi-bin/crop-amigo
<  value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
---
>  value: http://amigo1.geneontology.org/cgi-bin/amigo
>  value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
17c17
<  value: /data/www/planteome_dev/amigo/perl/bin
<  value: /data/www/planteome_dev2/amigo/perl/bin
---
---
>  value: /home/sjcarbon/local/src/git/amigo/perl/bin
>  value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
21c21
<  value: http://dev.planteome.org
<  value: http://test.planteome.org
---
---
>  value: http://localhost:9999
>  value: http://localhost:9999
33c33
32a33,37
<  value: http://dev.planteome.org/solr/
>    - model_annotation
>    - noctua_model_meta
>    - family
>    - general
>    - bbop_term_ac
40c45
<  value: http://galaxy.planteome.org/
---
---
>  value: http://localhost:8080/solr/
>  value: http://galaxy.berkeleybop.org/
37c37
42c47
<  value: /data/www/planteome_dev/amigo
<  comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
>  comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
<  value: http://test.planteome.org/solr/
---
>  value: http://dev.planteome.org/solr/
48c53
<  value: http://noctua.planteome.org/
---
>  value: http://noctua.berkeleybop.org/
52c57
<  value: /data/www/planteome_dev2/amigo
---
---
>  value: /home/sjcarbon/local/src/git/amigo
>  value: /home/sjcarbon/local/src/git/amigo
41c41
56c61
<  value: planteome-dev
<  value: test.planteome.org
---
---
>  value: localhost
>  value: localhost
45c45
60c65
<  value: /data/www/planteome_dev/amigo/static
<  value: /data/www/planteome_dev2/amigo/static
---
---
>  value: /home/sjcarbon/local/src/git/amigo/static
>  value: /home/sjcarbon/local/src/git/amigo/static
49c49
64c69
<  value: http://dev.planteome.org/static
<  value: http://test.planteome.org/static
---
---
>  value: http://localhost:9999/static
>  value: http://localhost:9999/static
53c53
68c73
<  value: 'all|[GPTE]O:[u0-9]{7}'
<  value: 'all|[PGTE]O:[0-9]{7}'
---
---
>  value: 'all|GO:[0-9]{7}'
>  value: 'all|GO:[0-9]{7}'
65c65
76c81
<  value: /data/www/planteome_dev/amigo/golr_timestamp.log
<  value: 1.0
---
---
>  value: /home/sjcarbon/local/src/git/amigo/golr_timestamp.log
>  value: 2.3.2
69c69
78c83
<  value: /data/planteome_dev/amigo/external/bbop.js
<  comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
---
>  value: /home/sjcarbon/local/src/git/amigo/external/bbop.js
>  comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
73c73
89,91c94,98
<   value: /data/www/planteome_dev/amigo/metadata
<    - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
<    - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
<     - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
---
>  value: /home/sjcarbon/local/src/git/amigo/metadata
>     - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
>    - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
>    - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
>    - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
>    - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
<    - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
<    - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
<    - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
<    - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
>    - '~/local/src/git/amigo/metadata/ont-config.yaml'
>    - '~/local/src/git/amigo/metadata/bio-config.yaml'
>    - '~/local/src/git/amigo/metadata/ann-config.yaml'
>    - '~/local/src/git/amigo/metadata/general-config.yaml'
>    - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
>    - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
>    - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
>    - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
<   value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
>  value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
<  value: /data/www/planteome_dev2/noctua-models/models/
---
>  value: '~/local/src/git/noctua-models/models/'
112c123
<    - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
>    - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
<  value: 20G
---
>  value: 3G
</pre>
</pre>


Now to run <pre>make install</pre>
Now to run <pre>npm install</pre>


This gives an error about a missing yui-compressor, so need to get that installed.
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>
Next problem is that rhino gives an error message about "invalid option modules".  Still communicating with Seth on solution.  Will update when solution found.
Solution was to comment out the test and docs part of the install target in the Makefile.  Rhino was apparently only used for unit testing, which we don't really need to do.


===Configure Apache2===
===Configure Apache2===
Line 250: Line 214:
<pre>ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
<pre>ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>
The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>


The proxy settings are to make it so the Server is able to talk to the SOLR data.
The proxy settings are to make it so the Server is able to talk to the SOLR data.
Line 257: Line 229:
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost


doing the <pre>make install</pre> now works without error.
===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>


However, the server doesn't work when navigated to.  It looks like a perl module is missing.  Installed the following via cpan:
===Load ontologies===
<pre>CGI::Application::Plugin::Forward</pre>
<pre>./node_modules/.bin/gulp load-ontology</pre>


Error is now about "Type of arg 1 to keys must be hash" Will work on this error.
===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>


This error apparently is the result of the older version of perl that we have installed.  Seth fixed this in git, so I did a git pull and got past it.


However, another perl module needed to be installed via cpan:
<pre>CGI::Application::Dispatch</pre>


At this point Amigo2 appears to be working.
At this point Amigo2 appears to be working.
Line 273: Line 244:




==Notes from older install that may still be relevant==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>
Again, earlier install had a missing perl module.  Installed the following via cpan:
<pre>CGI::Application::Plugin::Forward</pre>
<pre>CGI::Application::Dispatch</pre>
'''This page will be updated as I progress.'''
'''This page will be updated as I progress.'''

Revision as of 22:57, 12 November 2015

GOLR install:

Install the 3.6 version of SOLR

SOLR

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 /data/www/planteome_dev/SOLR/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 amigo]$ diff /etc/init.d/solr /etc/init.d/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 /data/www/planteome_dev/SOLR/example/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 -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++ --- > daemon --stop --name=solr --verbose

At this point, SOLR is now running. Next is to load data to it.

AmiGO2 install

Copy the example amigo.yaml file and make the following changes: 

 
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome 
5c5
<   value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
>   value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
<   value: /data/www/planteome_dev2/amigo/perl/bin
---
>   value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
<   value: http://test.planteome.org
---
>   value: http://localhost:9999
32a33,37
>     - model_annotation
>     - noctua_model_meta
>     - family
>     - general
>     - bbop_term_ac
40c45
<   value: http://galaxy.planteome.org/
---
>   value: http://galaxy.berkeleybop.org/
42c47
<   comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
>   comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
<   value: http://test.planteome.org/solr/
---
>   value: http://dev.planteome.org/solr/
48c53
<   value: http://noctua.planteome.org/
---
>   value: http://noctua.berkeleybop.org/
52c57
<   value: /data/www/planteome_dev2/amigo
---
>   value: /home/sjcarbon/local/src/git/amigo
56c61
<   value: test.planteome.org
---
>   value: localhost
60c65
<   value: /data/www/planteome_dev2/amigo/static
---
>   value: /home/sjcarbon/local/src/git/amigo/static
64c69
<   value: http://test.planteome.org/static
---
>   value: http://localhost:9999/static
68c73
<   value: 'all|[PGTE]O:[0-9]{7}'
---
>   value: 'all|GO:[0-9]{7}'
76c81
<   value: 1.0
---
>   value: 2.3.2
78c83
<   comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
>   comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
<     - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
<     - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
<     - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
>     - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
>     - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
>     - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
>     - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
>     - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
<     - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
<     - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
<     - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
<     - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
>     - '~/local/src/git/amigo/metadata/ont-config.yaml'
>     - '~/local/src/git/amigo/metadata/bio-config.yaml'
>     - '~/local/src/git/amigo/metadata/ann-config.yaml'
>     - '~/local/src/git/amigo/metadata/general-config.yaml'
>     - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
>     - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
>     - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
>     - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
<   value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
>   value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
<   value: /data/www/planteome_dev2/noctua-models/models/
---
>   value: '~/local/src/git/noctua-models/models/'
112c123
<     - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
>     - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
<   value: 20G
---
>   value: 3G

Now to run 

npm install


Configure Apache2

The Apache config file needs to be modified 

[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
<     ServerAdmin elserj@science.oregonstate.edu
<     ServerName dev.planteome.org
---
> <VirtualHost *:9999>
>     ServerAdmin sjcarbon@localhost
8c7
<     DocumentRoot /data/www/planteome_dev/amigo
---
>     DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
<     <Directory /data/www/planteome_dev/amigo/static>
---
>     <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
<       ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
>       ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
< 
<  ProxyRequests Off
<         <Proxy *>
<         Order deny,allow
<         Allow from 192.168.1.52
<         </Proxy>
< 
<     ProxyPass /solr http://localhost:8983/solr
<     ProxyPassReverse /solr http://localhost:8983/solr
< 
<     ErrorLog /data/www/planteome_dev/amigo/log/error.log
<     ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
>     ErrorLog /var/log/apache2/error.log
>     ScriptLog /var/log/apache2/cgi.log
65c54
<     CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
>     CustomLog /var/log/apache2/access.log combined

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way: 

ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm


The log files need to be created or else Apache will not start: 

mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section 

Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf

Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

Run amigo2 installer

./node_modules/.bin/gulp install

Load ontologies

./node_modules/.bin/gulp load-ontology

Load associations

./node_modules/.bin/gulp load-gafs


At this point Amigo2 appears to be working.



Notes from older install that may still be relevant

At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant) 

sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip

Create the following script in /usr/local/bin/yui-comprssor 

#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"

Make it executable with 

sudo chmod +x /usr/local/bin/yui-compressor


Again, earlier install had a missing perl module. Installed the following via cpan: 

CGI::Application::Plugin::Forward
CGI::Application::Dispatch

This page will be updated as I progress.

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