AmiGO2 install
From Planteome.org
Contents
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
<
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< 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
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< 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
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< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
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< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
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< value: http://test.planteome.org
---
> value: http://localhost:9999
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> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
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< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
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< 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.
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< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
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< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
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< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
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< value: test.planteome.org
---
> value: localhost
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< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
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< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
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< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
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< value: 1.0
---
> value: 2.3.2
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< 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.
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< - 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
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< - /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'
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< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
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< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
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< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
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< 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 nodejsNow to run
npm installto 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 installThere 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.
