picard installation failure

Question

[sanariyaz21]

hi

i am trying to install picard tools in my system

i tried installing and older version picardtools-1.128 simply by downloading it https://github.com/broadinstitute/picard/releases/tag/1.128 which didnt worked

so i downloaded latest release and gave the command as follows :

https://github.com/broadinstitute/picard
cd picard/
./gradlew shadowJar

but after this command i am getting the following error.

uhail@suhail-HP-Notebook:~/picard$ ./gradlew shadowJar

FAILURE: Build failed with an exception.

• Where: Build file '/home/suhail/picard/build.gradle' line: 55

• What went wrong: A problem occurred evaluating root project 'picard'.

  Cannot invoke method getURLs() on null object

• Try: Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Total time: 1.014 secs

i ahve tried installing older version picardtools-1.128 moved it to another directory and given the path but when executed the command it didnt worked too. for this package i used following commands:

chmod 755* (after goint in the directory)
cd ..
cp -r picard ~/software_library/
ln -sf ~/software_library/picard/picard.jar ~/software_library/bin/picard

but when executed :

suhail@suhail-HP-Notebook:~/Desktop/data/FAstq$ picard MarkDuplicates I=output.sort.bam O=output_marked.sort.bam M=picard_info.txt REMOVE_DUPLICATES=true AS=true
bash: /usr/bin/picard: No such file or directory

kindly help !!!!

[sanariyaz21]

it will be appreciated if somebody can just guide me with the installation commands as like many others i am new to ngs data analysis . help will be appreciated . thank you

[Pierre Lindenbaum]

simply by downloading it https://github.com/broadinstitute/picard/releases/tag/1.128 which didnt worked

what "it didn't worked" means ???

[sanariyaz21]

it didnt worked means as follows :

i ahve tried installing older version picardtools-1.128 moved it to another directory and given the path but when executed the command it didnt worked too. for this package i used following commands: chmod 755* (after goint in the directory) cd .. cp -r picard ~/software_library/ ln -sf ~/software_library/picard/picard.jar ~/software_library/bin/picard

but when executed : suhail@suhail-HP-Notebook:~/Desktop/data/FAstq$ picard MarkDuplicates I=output.sort.bam O=output_marked.sort.bam M=picard_info.txt REMOVE_DUPLICATES=true AS=true bash: /usr/bin/picard: No such file or directory

[Pierre Lindenbaum]

see my answer below

Futhermore:

 /usr/bin/picard: No such file or directory

means you have a basic $PATH problem...

Answer 1

[Pierre Lindenbaum]

. cp -r picard ~/software_library/ ln -sf ~/software_library/picard/picard.jar ~/software_library/bin/picard

this cannot work. picard.jar is not a standalone executable but a java jar : http://www.geeksforgeeks.org/jar-files-java/

you muts invoke it with java:

java -jar /path/to/picard.jar MarkDuplicates

[sanariyaz21]

thanks it worked i was not invoking it correctly. now its working well

Answer 2

[simon.vanheeringen]

Try using bioconda. After installation of Anaconda and setting up the bioconda repository, you can install Picard tools like this:

$ conda install picard

Answer 3

[genetic]

Hello,

I've invoke it with java, but I still have an error. Could you please let me know how should I fix this? Thank you.

[root@NGS:han]# java -jar picard.jar Exception in thread "main" java.lang.UnsupportedClassVersionError: picard/cmdline/PicardCommandLine : Unsupported major.minor version 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:803) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:442) at java.net.URLClassLoader.access$100(URLClassLoader.java:64) at java.net.URLClassLoader$1.run(URLClassLoader.java:354) at java.net.URLClassLoader$1.run(URLClassLoader.java:348) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:347) at java.lang.ClassLoader.loadClass(ClassLoader.java:425) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:312) at java.lang.ClassLoader.loadClass(ClassLoader.java:358) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

[Pierre Lindenbaum]

wong version of java (1.5). You need java (oracle)-1.8

[genetic]

Thank you. It works.

Answer 4

[gajularaviteja]

When ever iam trying to use picard it is waring thhat to upgrade my java version from 11 to 17 it is not ugrading the commanads which i used to upgrade is

sudo apt install openjdk-17-jdk-headless -y
sudo update-alternatives --config java   (Selected 17 version)
java -version
The output after checking the version is
(base) progenics@LAPTOP-IFCKMU88:~$ java -version
openjdk version "11.0.1-internal" 2018-10-16
OpenJDK Runtime Environment (build 11.0.1-internal+0-adhoc..src)
OpenJDK 64-Bit Server VM (build 11.0.1-internal+0-adhoc..src, mixed mode)

(base) progenics@LAPTOP-IFCKMU88:~$ picard -h /home/progenics/miniconda3/bin/picard: line 5: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory Error: LinkageError occurred while loading main class picard.cmdline.PicardCommandLine java.lang.UnsupportedClassVersionError: picard/cmdline/PicardCommandLine has been compiled by a more recent version of the Java Runtime (class file version 61.0), this version of the Java Runtime only recognizes class file versions up to 55.0

please help me in this Thank you!!

[Pierre Lindenbaum]

install openjdk-17

but your current java is still

openjdk version "11.0.1-internal" 2018-10-16

check the PATH, check the JAVA_HOME variable, remove the old version