trimmomatic excution error

Question

[sanariyaz21]

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

[sanariyaz21]

i request that kindly help me with this query

Answer 1

[Devon Ryan]

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

[sanariyaz21]

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

[GenoMax]

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

Answer 2

[Arup Ghosh]

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

[sanariyaz21]

thanks arup a lot . it worked .