Hi, Sridar,

Why use the FastQC directory -tool-data/shared/jars would make it easy to simply copy the way the current FastQC tool does this - the source for FastQC xml and python wrappers are easy to find in the central repository on bitbucket?

However, to do it properly so it's easy to autoinstall from a tool shed, please take a look at the test fastqc tool http://testtoolshed.g2.bx.psu.edu/view/fubar/fastqc repository which includes a tool_dependency.xml that autoinstalls the jar and sets up the path for a properly managed dependency - avoiding the ugly solution found in the existing fastqc tool. That's the way of the future for all tool wrappers, so a good thing to start using. Plenty of docs on the wiki and examples in the test toolshed.


On Fri, Jul 12, 2013 at 2:34 PM, sridhar srinivasan <sridhar2bioinfo@gmail.com> wrote:
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

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--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ