In this article, I will take you through the steps to install picard-tools on Ubuntu 20.04 LTS (Focal Fossa). picard-tools is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats like SAM/BAM/CRAM and VCF. It was started as a companion package to GATK so that GATK could concentrate on its core functions. Check more on official website. We will see the steps to install picard-tools on Ubuntu 20.04 LTS in great detail.

How to Install picard-tools on Ubuntu 20.04 LTS (Focal Fossa)

Also Read: How to Install uTorrent on Ubuntu 20.04 LTS (Focal Fossa)

Step 1: Prerequisites

a) You should have a running Ubuntu 20.04 LTS System.

b) You should have sudo or root access to run privileged commands.

c) You should have apt-get utility available in your System.

d) You should have Java 1.8 installed in your System.

 

Step 2: Update Your System

You can sync the System with the latest available updates from all the enabled repositories by using apt-get update command as shown below. If any of the packages need to be upgraded then do it by using apt-get upgrade command as shown below.

root@cyberithub:~# apt-get update
Hit:1 http://in.archive.ubuntu.com/ubuntu focal InRelease
Get:3 http://in.archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB]
Hit:4 http://ppa.launchpad.net/graphics-drivers/ppa/ubuntu focal InRelease
Get:5 http://in.archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB]
Hit:6 http://apt.postgresql.org/pub/repos/apt focal-pgdg InRelease
Get:7 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB]
Hit:8 http://ppa.launchpad.net/nilarimogard/webupd8/ubuntu focal InRelease
Get:9 https://repo.protonvpn.com/debian stable InRelease [2,519 B]
Hit:10 https://dl.google.com/linux/chrome/deb stable InRelease
Hit:11 http://download.opensuse.org/repositories/home:/selmf/xUbuntu_20.04 InRelease
Get:12 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [1,745 kB]
Hit:2 https://downloads.apache.org/cassandra/debian 40x InRelease
.......................................

 

Step 3: Install picard-tools

In the next step, you can install picard-tools by using apt-get install picard-tools command as shown below. This will download the tool along with all the additional required packages from Ubuntu repo.

root@cyberithub:~# apt-get install picard-tools
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following package was automatically installed and is no longer required:
libreadline5
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
ant ant-optional bzip2-doc gfortran gfortran-9 icu-devtools libactivation-java libaopalliance-java libapache-pom-java libargs4j-java libasm-java
libatinject-jsr330-api-java libbarclay-java libblas-dev libblas3 libbz2-dev libcdi-api-java libcglib-java libcodemodel-java libcommons-cli-java
libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java
libcommons-math3-java libcommons-parent-java libdom4j-java libdtd-parser-java libfastinfoset-java libfreemarker-java libgatk-native-bindings-java
libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgfortran-9-dev libgfortran5 libgkl-java libgkl-jni libgoogle-gson-java
libguava-java libguice-java libhawtjni-runtime-java libhtsjdk-java libhttpclient-java libhttpcore-java libicu-dev libistack-commons-java libjansi-java
libjansi-native-java libjaxb-api-java libjaxb-java libjaxen-java libjoptsimple-java libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libjsoup-java
libjsr305-java liblapack-dev liblapack3 liblightcouch-java liblog4j2-java liblzma-dev libmaven-file-management-java libmaven-parent-java
libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmongodb-java libngs-java libngs-sdk-dev libngs-sdk2
libpcre16-3 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpicard-java libplexus-archiver-java libplexus-cipher-java
libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java
libplexus-utils2-java libpng-dev libpng-tools libreadline-dev librelaxng-datatype-java librngom-java libsisu-guice-java libsisu-inject-java
libsisu-ioc-java libsisu-plexus-java libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libstax-ex-java libstreambuffer-java libtcl8.6 libtk8.6
libtxw2-java libwagon-http-java libwagon-provider-api-java libxml-commons-resolver1.1-java libxsom-java libxz-java r-base-core r-base-dev r-cran-boot
r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme
r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended
................................................

 

Step 4: Check all the available programs

You can check all the programs available with picard-tools command set by using picard-tools -h command as shown below.

root@cyberithub:~# picard-tools -h

Available Programs:
--------------------------------------------------------------------------------------
Base Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters
CheckIlluminaDirectory Asserts the validity for specified Illumina basecalling data.
CollectIlluminaBasecallingMetrics Collects Illumina Basecalling metrics for a sequencing run.
CollectIlluminaLaneMetrics Collects Illumina lane metrics for the given BaseCalling analysis directory.
ExtractIlluminaBarcodes Tool determines the barcode for each read in an Illumina lane.
IlluminaBasecallsToFastq Generate FASTQ file(s) from Illumina basecall read data.
IlluminaBasecallsToSam Transforms raw Illumina sequencing data into an unmapped SAM or BAM file.
MarkIlluminaAdapters Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.
......................................

 

Step 5: Uninstall picard-tools

Once you are done with picard-tools, you can choose to uninstall it from your system by using apt-get remove picard-tools command as shown below.

root@cyberithub:~# apt-get remove picard-tools
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
ant ant-optional gfortran gfortran-9 icu-devtools libactivation-java libaopalliance-java libapache-pom-java libargs4j-java libasm-java
libatinject-jsr330-api-java libbarclay-java libblas-dev libblas3 libbz2-dev libcdi-api-java libcglib-java libcodemodel-java libcommons-cli-java
libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java
libcommons-math3-java libcommons-parent-java libdom4j-java libdtd-parser-java libfastinfoset-java libfreemarker-java libgatk-native-bindings-java
libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgfortran-9-dev libgfortran5 libgkl-java libgkl-jni libgoogle-gson-java
libguava-java libguice-java libhawtjni-runtime-java libhtsjdk-java libhttpclient-java libhttpcore-java libicu-dev libistack-commons-java libjansi-java
libjansi-native-java libjaxb-api-java libjaxb-java libjaxen-java libjoptsimple-java libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libjsoup-java
libjsr305-java liblapack-dev liblapack3 liblightcouch-java liblog4j2-java liblzma-dev libmaven-file-management-java libmaven-parent-java
libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmongodb-java libngs-java libngs-sdk-dev libngs-sdk2
libpcre16-3 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpicard-java libplexus-archiver-java libplexus-cipher-java
libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java
libplexus-utils2-java libpng-dev libpng-tools libreadline-dev libreadline5 librelaxng-datatype-java librngom-java libsisu-guice-java libsisu-inject-java
libsisu-ioc-java libsisu-plexus-java libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libstax-ex-java libstreambuffer-java libtcl8.6 libtk8.6
libtxw2-java libwagon-http-java libwagon-provider-api-java libxml-commons-resolver1.1-java libxsom-java libxz-java r-base-core r-base-dev r-cran-boot
r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme
r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended
Use 'apt autoremove' to remove them.
The following packages will be REMOVED:
picard-tools
0 upgraded, 0 newly installed, 1 to remove and 25 not upgraded.
After this operation, 334 kB disk space will be freed.
Do you want to continue? [Y/n] Y
(Reading database ... 205888 files and directories currently installed.)
Removing picard-tools (2.18.25+dfsg-2) ...
Processing triggers for man-db (2.9.1-1) ...