This page was last updated on Tuesday, 16-Dec-2014 13:23:25 CST

Installation notes for Trimmomatic version 0.32

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Prerequisites

Java

Installation

1. $ ver="0.32"
2. $ cd /programinstallers/
3. $ wget -N http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-$ver.zip
4. $ cd /usr/local/bin
5. $ unzip /programinstallers/Trimmomatic-$ver.zip
   

   Archive:  /programinstallers/Trimmomatic-0.32.zip
      creating: Trimmomatic-0.32/
     inflating: Trimmomatic-0.32/LICENSE  
     inflating: Trimmomatic-0.32/trimmomatic-0.32.jar  
      creating: Trimmomatic-0.32/adapters/
     inflating: Trimmomatic-0.32/adapters/NexteraPE-PE.fa  
     inflating: Trimmomatic-0.32/adapters/TruSeq2-PE.fa  
     inflating: Trimmomatic-0.32/adapters/TruSeq2-SE.fa  
     inflating: Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa  
     inflating: Trimmomatic-0.32/adapters/TruSeq3-PE.fa  
     inflating: Trimmomatic-0.32/adapters/TruSeq3-SE.fa

6. Make a version-independent symlink
   $ ln -s Trimmomatic-$ver Trimmomatic
7. Make a trimmomatic wrapper script to launch the program
   $ nano trimmomatic
   

   # !/bin/bash
   type="$1"
   shift
   jar=`/bin/ls /usr/local/bin/Trimmomatic/trimmomatic-*.jar`
   if [ "$jar" == "" ]; then
     echo "Error, did not find jar file in /usr/local/bin/Trimmomatic"
     exit 1
   fi
   if [ "$type" == "PE" ]; then
     java -classpath $jar org.usadellab.trimmomatic.TrimmomaticPE $@
   elif [ "$type" == "SE" ]; then
     java -classpath $jar org.usadellab.trimmomatic.TrimmomaticSE $@
   else
     echo "Error, first parameter must be either \"PE\" or \"SE\""
     echo "See  http://www.usadellab.org/cms/index.php?page=trimmomatic  for other parameters"
     exit 2
   fi

8. $ chmod +x /usr/local/bin/trimmomatic