backlocate errors out

[RamRS]

Hi,

I installed jvarkit and backlocate as described in the documentation. I also placed mysql-connector-java-5.1.31-bin.jar in a custom location and added the mysql.jar variable in build.properties to point to it. However, when I run echo -e "GLA\tA143P" | java -jar dist/backlocate.jar, I get the following error:

[INFO/BackLocate] 2014-09-11 09:55:34 "Starting JOB at Thu Sep 11 09:55:34 EDT 2014 com.github.lindenb.jvarkit.tools.backlocate.BackLocate version=796ed1daa01c438fe99027105e17588a82e764f0  built=2014-07-10 12:25:05"
[INFO/BackLocate] 2014-09-11 09:55:34 "Command Line args : (EMPTY/NO-ARGS)"
[INFO/BackLocate] 2014-09-11 09:55:34 "Executing as ram@alphagala.1425mad.mssm.edu on Mac OS X 10.9.4 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_65-b14-466.1-11M4716"
[SEVERE/BackLocate] 2014-09-11 09:55:34 "com.mysql.jdbc.Driver"
java.lang.ClassNotFoundException: com.mysql.jdbc.Driver
    at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:171)
    at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.doWork(BackLocate.java:557)
    at com.github.lindenb.jvarkit.util.AbstractCommandLineProgram.instanceMain(AbstractCommandLineProgram.java:456)
    at com.github.lindenb.jvarkit.util.AbstractCommandLineProgram.instanceMainWithExit(AbstractCommandLineProgram.java:470)
    at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.main(BackLocate.java:634)
[SEVERE/BackLocate] 2014-09-11 09:55:34 "cannot.load.mysql.driver"
Exception in thread "main" java.lang.NoClassDefFoundError: htsjdk/samtools/util/CloserUtil
    at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.doWork(BackLocate.java:629)
    at com.github.lindenb.jvarkit.util.AbstractCommandLineProgram.instanceMain(AbstractCommandLineProgram.java:456)
    at com.github.lindenb.jvarkit.util.AbstractCommandLineProgram.instanceMainWithExit(AbstractCommandLineProgram.java:470)
    at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.main(BackLocate.java:634)
Caused by: java.lang.ClassNotFoundException: htsjdk.samtools.util.CloserUtil
    at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
    ... 4 more

How would I address this please? Thank you!

[lindenb]

There's not only mysql. it looks like you're missing all the libraries required (htsjdk... ). Check your paths, did you install htsjdk ? did you compile after editing build.properties ?

• can you try this (of course, replace the paths with your context )

$ cd jvarkit
$ ant backlocate
$ cd dist
$ echo "#" | java -cp /home/lindenb/package/mysql-connector-java-5.1.12/mysql-connector-java-5.1.12-bin.jar::/home/lindenb/src/jvarkit-git/htsjdk/dist/apache-ant-1.8.2-bzip2.jar:/home/lindenb/src/jvarkit-git/htsjdk/dist/htsjdk-1.117.jar:/home/lindenb/src/jvarkit-git/htsjdk/dist/snappy-java-1.0.3-rc3.jar:/home/lindenb/src/jvarkit-git/htsjdk/dist/commons-jexl-2.1.1.jar:/home/lindenb/src/jvarkit-git/htsjdk/dist/commons-logging-1.1.1.jar:backlocate.jar com.github.lindenb.jvarkit.tools.backlocate.BackLocate

[RamRS]

Ah, I compliled before editing build.properties. I'll also check on building htsjdk.

[RamRS]

I compiled again and it works. Thank you so much, @lindenb !