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DEPENDENCIES.md

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TNRS DEPENDENCIES

The following instructions can be used to install TNRS dependencies on a CentOS 5.8 system such as the iPlant Atmosphere base VM (image ID: emi-F1F122E4).

Some links may be unavailable. Please visit the specific developer's home page to locate the required files.

Instructions are given for the components listed below

  1. Git 1.7.4 or higher
  2. MySQL 5.0.95 or higher
  3. PHP 5.3.3 or higher, including mysql and mbstring
  4. Maven 2.2.1 or higher
  5. Apache Tomcat 7.0.33 or higher
  6. Apache JK Modules 1.2.31 or higher
  7. YAML 0.1.4
  8. Ruby 1.9.3 or higher
  9. Rubygems 1.8.23 or higher

Apache HTTP Server 2.2.3 or higher and Java 1.6 are already available on the VM image.

SYSTEM SETUP

a. Gain root access

sudo su -

b. Remove graphic features

yum groupremove 'GNOME Desktop Environment' -y

c. Upgrade the system

yum upgrade -y

##1. Git >=1.7.4

yum install git -y

##2. MySQL >=5.0.95

yum install mysql-server -y

##3. PHP >=5.3.3

yum remove php.x86_64 -y
yum remove php-cli.x86_64 -y
yum remove php-common.x86_64 -y
yum install php53 -y

###3.1. PHP mysql extension >=5.3.3

yum install php53-mysql -y

###3.2. PHP mbstring (multi-byte string handling) extension >=5.3.3

yum install php53-mbstring -y

##4. Maven >=2.2.1

wget http://mirrors.ibiblio.org/apache/maven/maven-2/2.2.1/binaries/apache-maven-2.2.1-bin.tar.gz
tar -xf apache-maven-2.2.1-bin.tar.gz
mv apache-maven-2.2.1 /opt/
ln -s /opt/apache-maven-2.2.1/ /opt/maven

echo "
	export M2_HOME=/opt/maven
	export M2=\$M2_HOME/bin
	export PATH=\$M2:\$PATH" >>/etc/profile.d/maven.sh
chmod 755 /etc/profile.d/maven.sh
source /etc/profile.d/maven.sh

Note: Add a mirror to Maven's setting file ~/.m2/settings.xml

cd
mkdir .m2
cd .m2
echo '<settings xmlns="http://maven.apache.org/SETTINGS/1.1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http:// maven.apache.org/SETTINGS/1.1.0 http://maven.apache.org/xsd/settings-1.1.0.xsd">
	   <mirrors>
	       <mirror>
               <id>jboss-public</id>
               <name>JBoss Public Nexus Repository</name>
               <url>https://repository.jboss.org/nexus/content/groups/public/</url>
               <mirrorOf>jboss</mirrorOf>
     	  </mirror>
	   </mirrors>
</settings>
' >> settings.xml

##5. Apache Tomcat >=7.0.33 cd /tmp wget http://mirror.cc.columbia.edu/pub/software/apache/tomcat/tomcat-7/v7.0.33/bin/apache-tomcat-7.0.33.tar.gz tar -xf apache-tomcat-7.0.33.tar.gz mv apache-tomcat-7.0.33 /opt ln -s /opt/apache-tomcat-7.0.33 /opt/tomcat

##6. Apache JK Modules >= 1.2.31

wget http://archive.apache.org/dist/tomcat/tomcat-connectors/jk/binaries/linux/jk-1.2.31/x86_64/mod_jk-1.2.31-httpd-2.2.x.so
cp mod_jk-1.2.31-httpd-2.2.x.so /etc/httpd/modules/mod_jk.so
chmod 755 /etc/httpd/modules/mod_jk.so

##7. YAML 0.1.4

wget http://pyyaml.org/download/libyaml/yaml-0.1.4.tar.gz
tar xzvf yaml-0.1.4.tar.gz
cd yaml-0.1.4
./configure
make
make install
cd ..

##8. Ruby >=1.9.3

wget http://ftp.ruby-lang.org/pub/ruby/1.9/ruby-1.9.3-p194.tar.gz
tar -xf ruby-1.9.3-p194.tar.gz
cd ruby-1.9.3-p194
./configure
make
make test
make install
cd ..

##9. Rubygems >=1.8.23

gem update