how to install picard and GATK

Question

[adR]

Hi all

I want to install the current version of the picard and GATK software using Ubuntu terminal on windows PC for some genomics analysis. I have the current version java but could not able to install picard. Well I download the entire folder from https://github.com/broadinstitute/picard/releases/tag/2.26.5 and followed the instruction written in the readme but its not in my system.

So would you please advise me how I can get it?

Best, AD

Answer 1

[Pierre Lindenbaum]

wget -O picard.jar "https://github.com/broadinstitute/picard/releases/download/2.26.5/picard.jar"
java -jar picard.jar

[adR]

@Pierre Lindenbaum, Thank you so much! It just worked! Would you also show for Genome Analysis Toolkit (GATK)?

[Pierre Lindenbaum]

show us what you tried.

[adR]

Basically followed your example and it goes well

   wget https://github.com/broadinstitute/gatk/releases/download/4.2.3.0/gatk-4.2.3.0.zip
    unzip gatk-4.2.3.0.zip
    cd  gatk-4.2.3.0
    java -jar gatk-package-4.2.3.0-local.jar

However, testing the the spark, it compline as below.

java -jar gatk-package-4.2.3.0-spark.jar
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/spark/Partitioner
        at java.base/java.lang.Class.getDeclaredConstructors0(Native Method)
        at java.base/java.lang.Class.privateGetDeclaredConstructors(Class.java:3137)
        at java.base/java.lang.Class.getConstructors(Class.java:1943)
        at org.broadinstitute.hellbender.utils.ClassUtils.canMakeInstances(ClassUtils.java:31)
        at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main.java:319)
        at org.broadinstitute.hellbender.Main.setupConfigAndExtractProgram(Main.java:180)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:202)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.lang.ClassNotFoundException: org.apache.spark.Partitioner
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
        at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)

Thanks for your help!

[Pierre Lindenbaum]

why would you need spark ?