Dear Developers,

I am using java jar files for softwares like fastqc, GATK. For running these tools i install the softare and set path in bash_profile file.

My doubt is i placed the jar files in galaxy dist folder (
galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
)

is this enough to call the jar files from galaxy??

After placing the jar file i tried running the tool using the interface it gives ERROR as

# FastQC cl = /illumina/data/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/illumina/data/galaxy/galaxy-dist/database/job_working_directory/000/216/dataset_546_files --f=bam /illumina/data/galaxy/galaxy-dist/database/job_working_directory/000/216/dataset_546_files/Bowtie2_on_data_7_and_data_6__aligned_reads


Exception in thread "main" java.lang.NoClassDefFoundError: uk/ac/babraham/FastQC/FastQCApplication

Caused by: java.lang.ClassNotFoundException: uk.ac.babraham.FastQC.FastQCApplication

	at java.net.URLClassLoader$1.run(URLClassLoader.java:217)


	at java.security.AccessController.doPrivileged(Native Method)

	at java.net.URLClassLoader.findClass(URLClassLoader.java:205)

	at java.lang.ClassLoader.loadClass(ClassLoader.java:321)

	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)


	at java.lang.ClassLoader.loadClass(ClassLoader.java:266)

Could not find the main class: uk.ac.babraham.FastQC.FastQCApplication. Program will exit.

I got same error for GATK also

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed

##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to 

##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-a3rr8t) does not exist.

##### ERROR -----------------------------------------------------------------------------------------



Could you please suggest on the same..


Thanks
Sridhar