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trimmomatic excution error

hi i have installed trimmomatic 0.36 on ubuntu 14.04 the following is the command i use : 

trimmomatic PE -threads 4 -phred33 DRR001913_1.fastq DRR001913_2.fastq  trimmed_DRR001913_1.fastq unpaired_DRR001913_1.fastq trimmed_DRR001913_2.fastq unpaired_DRR001913_2.fastq AVGQUAL:20 SLIDINGWINDOW:4:15 MINLEN:50
 error : trimmomatic: command not found

for installation i have used the following commands : downloaded from this link : www.usadellab.org/cms/index.php?page=trimmomatic

sudo apt-get install binfmt-support
cd Trimmomatic-0.36/
 chmod 755 trimmomatic-0.36.jar 
  cd ..
  cd Desktop/
  cp -r Trimmomatic-0.36/ ~/software_library/
  ln -sf ~/software_library/Trimmomatic-0.36//trimmomatic-0.36.jar ~/software_library/bin/trimmomatic

these are the commands i have used to install trimmomatic in my system ln -sf ~/software_library/Trimmomatic-0.36//trimmomatic-0.36.jar ~/software_library/bin/trimmomatic after the last command i do not recieve any error

how can i install it successfully

software error
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updated by Arup Ghosh Arup Ghosh • written by sanariyaz21 • sanariyaz21

i request that kindly help me with this query

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written by sanariyaz21 • sanariyaz21

2 answers

Apparently ~/software_library/bin/ isn't in your PATH. Change that and it will work.

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written by Devon Ryan Devon Ryan

what change should i do can you please suggest me in my path

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written by sanariyaz21 • sanariyaz21

Run this in the terminal where you are working: export PATH=$PATH:~/software_library/bin/

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written by GenoMax GenoMax

Try to run like example mentioned in Trimmomatic homepage.

http://www.usadellab.org/cms/index.php?page=trimmomatic

For the mentioned scenario the command will be like

java -jar ~/software_library/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 4 -phred33 DRR001913_1.fastq DRR001913_2.fastq trimmed_DRR001913_1.fastq unpaired_DRR001913_1.fastq trimmed_DRR001913_2.fastq unpaired_DRR001913_2.fastq AVGQUAL:20 SLIDINGWINDOW:4:15 MINLEN:50

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written by Arup Ghosh Arup Ghosh

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