Install Trimmomatic?

[Palgrave]

Hi all,

How did you build and install trimmomatic? There is no make file so I am not sure how to run the software. Anyone?

[westerman]

It is java based. The on-line web page should explain how to run it. I use:

java -Xms512m -Xmx2000m -classpath Trimmomatic-0.20/trimmomatic-0.20.jar org.usadellab.trimmomatic.TrimmomaticPE

[tonybolger]

How did you build and install trimmomatic? There is no make file so I am not sure how to run the software. Anyone?

It can be built from source using ant (the java near-equivalent of make), but i'd recommend using the binary download, which contains the pre-built jar.

Also, there is no installer, you can just copy the jar somewhere convenient - you need to refer to it using -classpath when running Trimmomatic.

[figo1019]

Hi all,

How did you build and install trimmomatic? There is no make file so I am not sure how to run the software. Anyone?

Hi

I am also facing the problem of installing the trimmomatic .I even tried the binary version but I am getting the error

"Failed to load Main-Class manifest attribute from trimmomatic-0.22.jar"

regards

[tonybolger]

I am also facing the problem of installing the trimmomatic .I even tried the binary version but I am getting the error

"Failed to load Main-Class manifest attribute from trimmomatic-0.22.jar"

Unfortunately, since there are 2 main classes, it is not possible to run trimmomatic via the -jar option.

For paired end mode, you need: java -classpath <path to trimmomatic jar> org.usadellab.trimmomatic.TrimmomaticPE ...

For single end mode: java -classpath <path to trimmomatic jar> org.usadellab.trimmomatic.TrimmomaticSE ...

The full deatils are here

[Susanna5]

It can be built from source using ant (the java near-equivalent of make), but i'd recommend using the binary download, which contains the pre-built jar.

Also, there is no installer, you can just copy the jar somewhere convenient - you need to refer to it using -classpath when running Trimmomatic.

Also had a problem with the download from source.. Easiest solution is indeed, download in binary. Problems solved

[elli]

...I have the same problem!

I also installed the binary version and after placing the command to run the program I get the following error:

Error: Invalid or corrupt jarfile /home/feindt/programs/trimmomatic-0.30

Does anybody have suggestions what to do?
Thanks!

[winsettz]

An example of my shell script that I use to kick off Trimmomatic jobs (derived from Trimmomatic-0.30.zip)

ADAPTER=TruSeq3
ORIENTATION=PE #or SE
java -jar /data5/Programs/Trimmomatic-0.30/trimmomatic-0.30.jar $ORIENTATION -threads 4 -phred33 $1 $2  $1.1P_$ADAPTER.fastq $1.1U_$ADAPTER.fastq $2.2P_$ADAPTER.fastq $2.2U_$ADAPTER.fastq ILLUMINACLIP:/data5/Programs/Trimmomatic-0.30/adapters/$ADAPTER\-$ORIENTATION.fa:2:30:10 LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:36

$1, $2 are the options fed to the shellscript, so it's

./shell file1.fastq file2.fastq, and then its off to the races.

[tingxiang]

Hi all,

I'm trying to install Trimmomatic. I follow this website: http://www.personal.psu.edu/iua1/cou...tory-2014.html

It says to install, type cd ~/src. When I did, the error appeared:-

-bash: cd: /Users/tinaneik/src: No such file or directory

What should I do?

Cheers,
Tina

[GenoMax]

Hi all,

I'm trying to install Trimmomatic. I follow this website: http://www.personal.psu.edu/iua1/cou...tory-2014.html

It says to install, type cd ~/src. When I did, the error appeared:-

-bash: cd: /Users/tinaneik/src: No such file or directory

What should I do?

Cheers,
Tina

In the example, you linked a directory called "src" is used to download code locally. You will need to make this directory under /Users/tinaneik if you want to follow the guide as is.

$ mkdir /Users/tinaneik/src

OR

$ mkdir ~/src

[tingxiang]

Thanks. I typed mkdir /Users/tinaneik/src as recommended, is says:

mkdir: /Users/tinaneik/src: File exists

Then, I typed cd ~src, again the error appeared:

-bash: cd: /Users/tinaneik/src: No such file or directory

Any reason?