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3.5 years ago
robbenstijn
•
0
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
