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DEPENDENCIES
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DEPENDENCIES
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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. Java 1.7.0 or higher
2. Git 1.7.4 or higher
3. MySQL 5.0.95 or higher
4. PHP 5.3.3 or higher, including mysql and mbstring
5. Maven 2.2.1 or higher
6. Apache Tomcat 7.0.33 or higher
7. Apache JK Modules 1.2.31 or higher
8. YAML 0.1.4
9. Ruby 1.9.3 or higher
10. Rubygems 1.8.23 or higher
Apache HTTP Server 2.2.3 or higher is 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. Java JDK >=1.7.0
Note: It is necessary to obtain Java JDK 1.7 RPM from Oracle: http://www.oracle.com/technetwork/java/javase/downloads/index.html
yum groupremove java -y
yum remove java-1.6.0-openjdk -y
rpm -ivh jdk-7-linux-x64.rpm
echo 'export JAVA_HOME=/usr/java/latest
export JRE_HOME=$JAVA_HOME/jre
export PATH=$PATH:$JAVA_HOME/bin
' >>/etc/profile.d/java.sh
chmod 755 /etc/profile.d/java.sh
source /etc/profile.d/java.sh
---
---
2. Git >=1.7.4
yum install git -y
---
---
3. MySQL >=5.0.95
yum install mysql-server -y
---
---
4. 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
-PHP mysql extension >=5.3.3
yum install php53-mysql -y
-PHP mbstring (multi-byte string handling) extension >=5.3.3
yum install php53-mbstring -y
---
---
5. 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
---
---
6. 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
---
---
7. 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
---
---
8. 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 ..
---
---
9. 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 ..
---
---
10. Rubygems >=1.8.23
gem update
---