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>
mvn clean package
</pre>
This will take about half an hour.


===SOLR===
===SOLR===
Line 27: Line 12:
<pre>
<pre>
cd /data/www/planteome_dev
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
git clone https://github.com/planteome/amigo.git amigo
</pre>
</pre>


Go back to the SOLR directory and replace the config with those from GOLR:
Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
<pre>
cd /lemma/justin/SOLR/apache-solr-3.6.2/example/solr/conf
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp solrconfig.xml solrconfig.xml.org
Line 47: Line 32:
</pre>
</pre>


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):
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).  Pick either the systemd or init.d version, depending on which init system is being used:
 
systemd version:
<pre>
[elserj@floret extensions]$ cat /etc/systemd/system/solr.service
[Unit]
Description=Apache Solr
After=syslog.target network.target remote-fs.target nss-lookup.target
 
[Service]
Type=simple
WorkingDirectory=/data/www/planteome/SOLR/example
ExecStart=/usr/bin/java -jar /data/www/planteome/SOLR/example/start.jar
Restart=on-failure


[Install]
WantedBy=multi-user.target
</pre>
init.d version:
Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]
Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]


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>
<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 60: Line 63:
<  
<  
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
</pre>


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://localhost:8983
---
> 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
33c33
21c21
<  value: http://localhost:8983/solr/
<  value: http://test.planteome.org
---
---
>  value: http://localhost:8080/solr/
>  value: http://localhost:9999
37c37
32a33,37
<  value: /data/www/planteome_dev/amigo
>    - 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
>  value: /home/sjcarbon/local/src/git/amigo
41c41
56c61
<  value: planteome-dev
<  value: test.planteome.org
---
---
>  value: localhost
>  value: localhost
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<  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
53c53
64c69
<  value: 'all|[GPTE]O:[u0-9]{7}'
<  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}'
>  value: 'all|GO:[0-9]{7}'
65c65
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<  value: /data/www/planteome_dev/amigo/golr_timestamp.log
<  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.'
---
---
>  value: /home/sjcarbon/local/src/git/amigo/golr_timestamp.log
>  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.
69c69
89,91c94,98
<   value: /data/planteome_dev/amigo/external/bbop.js
<    - 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/external/bbop.js
>     - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
73c73
>    - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
<   value: /data/www/planteome_dev/amigo/metadata
>    - 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
---
---
>  value: /home/sjcarbon/local/src/git/amigo/metadata
>     - '~/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>
Next is to install nodejs (if it isn't already)


This gives an error about a missing yui-compressor, so need to get that installed.
On CentOS 6:
<pre>
<pre>sudo su -
sudo mkdir /usr/local/share/yui-compressor
curl --silent --location https://rpm.nodesource.com/setup | bash -
sudo chown elserj: /usr/local/share/yui-compressor
yum install nodejs</pre>
cd /usr/local/share/yui-compressor
Now to run <pre>npm install</pre> to install necessary nodejs modules.
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 197: Line 195:
The Apache config file needs to be modified
The Apache config file needs to be modified
<pre>
<pre>
[elserj@palea amigo]$ diff conf/amigo2-apache.conf conf/amigo2-apache.conf.bla
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,3c2,3
2,4c2,3
< <VirtualHost *:9999>
< <VirtualHost *:80>
<    ServerAdmin sjcarbon@localhost
<    ServerAdmin elserj@science.oregonstate.edu
<    ServerName dev.planteome.org
---
---
> <VirtualHost *:80>
> <VirtualHost *:9999>
>    ServerAdmin elserj@localhost
>    ServerAdmin sjcarbon@localhost
>    ServerName dev.planteome.org
8c7
7c7
<    DocumentRoot /data/www/planteome_dev/amigo
<    DocumentRoot /home/sjcarbon/local/src/git/amigo
---
---
>    DocumentRoot /data/www/planteome_dev/amigo
>    DocumentRoot /home/sjcarbon/local/src/git/amigo
10c10
11c10
<    <Directory /home/sjcarbon/local/src/git/amigo/static>
<    <Directory /data/www/planteome_dev/amigo/static>
---
---
>    <Directory /data/www/planteome_dev/amigo/static>
>    <Directory /home/sjcarbon/local/src/git/amigo/static>
19c19
20c19
<      ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
<      ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
---
>      ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
>      ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
47,48c47,48
48,59c47,48
<    ErrorLog /var/log/apache2/error.log
<
<    ScriptLog /var/log/apache2/cgi.log
<  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 /data/www/planteome_dev/amigo/log/error.log
>    ErrorLog /var/log/apache2/error.log
>    ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
>    ScriptLog /var/log/apache2/cgi.log
54c54
65c54
<    CustomLog /var/log/apache2/access.log combined
<    CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
---
>    CustomLog /data/www/planteome_dev/amigo/log/access.log combined</pre>
>    CustomLog /var/log/apache2/access.log combined</pre>


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:
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:
<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>wget 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.


I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
Line 236: Line 254:
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>
 
There may be some missing perl packages here. I had to install <pre>Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
CGI::Application::Dispatch
CGI::Application::Plugin::Forward
CGI::Application::Plugin::Session
CGI::Application::Plugin::TT
CGI::Application::Plugin::Redirect
DBI
Data::FormValidator
Graph::Directed
XML::Parser
XML::XPath
GraphViz
DBD::SQLite
</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.


==Notes from older install==
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>




'''This page will be updated as I progress.'''
'''This page will be updated as I progress.'''

Latest revision as of 18:46, 2 November 2016

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/planteome/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). Pick either the systemd or init.d version, depending on which init system is being used:

systemd version: 

[elserj@floret extensions]$ cat /etc/systemd/system/solr.service 
[Unit]
Description=Apache Solr
After=syslog.target network.target remote-fs.target nss-lookup.target

[Service]
Type=simple
WorkingDirectory=/data/www/planteome/SOLR/example
ExecStart=/usr/bin/java -jar /data/www/planteome/SOLR/example/start.jar
Restart=on-failure

[Install]
WantedBy=multi-user.target

init.d version: 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

Next is to install nodejs (if it isn't already)

On CentOS 6: 

sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs

Now to run 

npm install

to install necessary nodejs modules.


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: 

wget 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

There may be some missing perl packages here. I had to install 

Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
CGI::Application::Dispatch
CGI::Application::Plugin::Forward
CGI::Application::Plugin::Session
CGI::Application::Plugin::TT
CGI::Application::Plugin::Redirect
DBI
Data::FormValidator
Graph::Directed
XML::Parser
XML::XPath
GraphViz
DBD::SQLite

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

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


This page will be updated as I progress.

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