How To Install picard-tools on Ubuntu 20.04
Introduction
In this tutorial we learn how to install picard-tools on Ubuntu 20.04.
What is picard-tools
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
There are three methods to install picard-tools on Ubuntu 20.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install picard-tools Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install picard-tools using apt-get by running the following command:
sudo apt-get -y install picard-tools
Install picard-tools Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install picard-tools using apt by running the following command:
sudo apt -y install picard-tools
Install picard-tools Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install picard-tools using aptitude by running the following command:
sudo aptitude -y install picard-tools
How To Uninstall picard-tools on Ubuntu 20.04
To uninstall only the picard-tools package we can use the following command:
sudo apt-get remove picard-tools
Uninstall picard-tools And Its Dependencies
To uninstall picard-tools and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove picard-tools
Remove picard-tools Configurations and Data
To remove picard-tools configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge picard-tools
Remove picard-tools configuration, data, and all of its dependencies
We can use the following command to remove picard-tools configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge picard-tools
References
Summary
In this tutorial we learn how to install picard-tools package on Ubuntu 20.04 using different package management tools: apt, apt-get and aptitude.
