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 <
sridhar2bioi...@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
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