Trimmomatic installation makefile error

Question

[robbenstijn]

I am trying to install this trimmomatic file on my remote server (linux): https://github.com/timflutre/trimmomatic

Whenever I proceed with the install protocol and enter the make command (as specified in the README file) I get the following error:

cd src/; javac -classpath ".:../lib/jbzip2-0.9.jar" -d ../classes org/usadellab/                                                                                                                                       trimmomatic/Trimmomatic.java org/usadellab/trimmomatic/trim/ToPhred64Trimmer.jav                                                                                                                                       a org/usadellab/trimmomatic/trim/SlidingWindowTrimmer.java org/usadellab/trimmom                                                                                                                                       atic/trim/ToPhred33Trimmer.java org/usadellab/trimmomatic/trim/MaximumInformatio                                                                                                                                       nTrimmer.java org/usadellab/trimmomatic/trim/CropTrimmer.java org/usadellab/trim                                                                                                                                       momatic/trim/LeadingTrimmer.java org/usadellab/trimmomatic/trim/Trimmer.java org                                                                                                                                       /usadellab/trimmomatic/trim/AvgQualTrimmer.java org/usadellab/trimmomatic/trim/M                                                                                                                                       inLenTrimmer.java org/usadellab/trimmomatic/trim/TrimmerFactory.java org/usadell                                                                                                                                       ab/trimmomatic/trim/BarcodeSplitter.java org/usadellab/trimmomatic/trim/Trailing                                                                                                                                       Trimmer.java org/usadellab/trimmomatic/trim/IlluminaClippingTrimmer.java org/usa                                                                                                                                       dellab/trimmomatic/trim/HeadCropTrimmer.java org/usadellab/trimmomatic/trim/Abst                                                                                                                                       ractSingleRecordTrimmer.java org/usadellab/trimmomatic/fasta/FastaParser.java or                                                                                                                                       g/usadellab/trimmomatic/fasta/FastaSerializer.java org/usadellab/trimmomatic/fas                                                                                                                                       ta/FastaRecord.java org/usadellab/trimmomatic/TrimmomaticPE.java org/usadellab/t                                                                                                                                       rimmomatic/threading/BlockOfWork.java org/usadellab/trimmomatic/threading/TrimLo                                                                                                                                       gRecord.java org/usadellab/trimmomatic/threading/ParserWorker.java org/usadellab                                                                                                                                       /trimmomatic/threading/TrimLogWorker.java org/usadellab/trimmomatic/threading/Tr                                                                                                                                       imStatsWorker.java org/usadellab/trimmomatic/threading/SerializerWorker.java org                                                                                                                                       /usadellab/trimmomatic/threading/BlockOfRecords.java org/usadellab/trimmomatic/u                                                                                                                                       til/PositionTrackingInputStream.java org/usadellab/trimmomatic/util/ConcatGZIPIn                                                                                                                                       putStream.java org/usadellab/trimmomatic/Pairomatic.java org/usadellab/trimmomat                                                                                                                                       ic/fastq/FastqSerializer.java org/usadellab/trimmomatic/fastq/FastqRecord.java o                                                                                                                                       rg/usadellab/trimmomatic/fastq/FastqParser.java org/usadellab/trimmomatic/Trimmo                                                                                                                                       maticSE.java org/usadellab/trimmomatic/TrimStats.java; \
cd ../classes; jar xf ../lib/jbzip2-0.9.jar; \
jar cmf ../MANIFEST.MF trimmomatic.jar ./
/bin/sh: 2: javac: not found
/bin/sh: 3: jar: not found
/bin/sh: 4: jar: not found
Makefile:7: recipe for target 'all' failed
make: *** [all] Error 127

I suspect this has something to do with Java but I am uncertain how to tackle this problem. Does anyone know how to address these kinds of errors?

Any help is much appreciated!

Kind regards

Answer 1

[Pierre Lindenbaum]

install a java runtime (like openjdk version >=8) and update your PATH if needed.