picard-tools command not found

In this troubleshooting guide we learn how to fix picard-tools command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

picard-tools: command not found

or when using sudo you get the following error message

sudo: picard-tools: command not found

Solutions to picard-tools: command not found

How To Fix picard-tools: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu picard-tools is provided by picard-tools package.

picard-tools is:

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Picard Tools includes these utilities to manipulate SAM and BAM files: AddCommentsToBam FifoBuffer AddOrReplaceReadGroups FilterSamReads BaitDesigner FilterVcf BamIndexStats FixMateInformation BamToBfq GatherBamFiles BedToIntervalList GatherVcfs BuildBamIndex GenotypeConcordance CalculateHsMetrics IlluminaBasecallsToFastq CalculateReadGroupChecksum IlluminaBasecallsToSam CheckIlluminaDirectory LiftOverIntervalList CheckTerminatorBlock LiftoverVcf CleanSam MakeSitesOnlyVcf CollectAlignmentSummaryMetrics MarkDuplicates CollectBaseDistributionByCycle MarkDuplicatesWithMateCigar CollectGcBiasMetrics MarkIlluminaAdapters CollectHiSeqXPfFailMetrics MeanQualityByCycle CollectIlluminaBasecallingMetrics MergeBamAlignment CollectIlluminaLaneMetrics MergeSamFiles CollectInsertSizeMetrics MergeVcfs CollectJumpingLibraryMetrics NormalizeFasta CollectMultipleMetrics PositionBasedDownsampleSam CollectOxoGMetrics QualityScoreDistribution CollectQualityYieldMetrics RenameSampleInVcf CollectRawWgsMetrics ReorderSam CollectRnaSeqMetrics ReplaceSamHeader CollectRrbsMetrics RevertOriginalBaseQualitiesAndAddMateCigar CollectSequencingArtifactMetrics RevertSam CollectTargetedPcrMetrics SamFormatConverter CollectVariantCallingMetrics SamToFastq CollectWgsMetrics ScatterIntervalsByNs CompareMetrics SortSam CompareSAMs SortVcf ConvertSequencingArtifactToOxoG SplitSamByLibrary CreateSequenceDictionary SplitVcfs DownsampleSam UpdateVcfSequenceDictionary EstimateLibraryComplexity ValidateSamFile ExtractIlluminaBarcodes VcfFormatConverter ExtractSequences VcfToIntervalList FastqToSam ViewSam

To fix this problem, we can install more using the command below.

sudo apt-get -y install picard-tools

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install picard-tools.

sudo apt -y install picard-tools

Or if you have aptitude installed you can use the following command.

sudo aptitude install picard-tools

Summary

In this tutorial we learn how to fix picard-tools command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.