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 followin 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.