Trimmomatic .jar not included anymore?

Question

[Emily]

I tried to run Trimmomatic 0.39 but ran into Error: Invalid or corrupt jarfile /storage/home/user/tools/Trimmomatic-0.39/. I went into the Trimmomatic directory and noticed that the decompressed binary .jar was not created at all. Java is updated to the latest version.

I configured my PATH for this tool export PATH=/storage/home/user/tools/Trimmomatic-0.39/:$PATH even tried export PATH=/storage/home/user/tools/Trimmomatic-0.39/adapters:$PATH and run trimmomatic but still failed....

The command I used to run trimmomatic is this java -jar /storage/home/user/tools/Trimmomatic-0.39/ SE -phred33 S23_R1_001_.fastq.gz S23_R1_001_OP.fastq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

also tried this way java -jar /storage/home/user/tools/Trimmomatic-0.39/adapters SE -phred33 3159_S23_R1_001_.fastq.gz 3159_S23_R1_001_.fastq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 after setting PATH to the adapters directory, still was not working...

Not sure where I did it wrong and why .jar was not there when I downloaded it or if missed something on my end. Note, the file is single-end read.

Any advice is appreciated.

Thank you.

[Pierre Lindenbaum]

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[Emily]

Done, thank you!

Answer 1

[petebio]

I am guessing that you actually downloaded the source files and not the compiled binary which is why you are missing the .jar file? If this is the case, then you should just re-download the binary directly from the Usadel lab website and get the binary for version 0.39.

[Emily]

I think that solved it, should have gotten it from their website instead of their GitHub. thank you.

Answer 2

[Pierre Lindenbaum]

The command I used to run trimmomatic is this java -jar /storage/home/sjw6257/tools/Trimmomatic-0.39/

java -jar argument should be a file with a .jar suffix not a directory like ' /storage/home/sjw6257/tools/Trimmomatic-0.39/' . Look into that directory if the jar is present and use it.