Hello Ross,
Thanks for the reply..

i copied the source directory to tool-data/shared/jars

now it works for the fastqc..

I tried the same for GATK copied the source directory t the location
tool-data/shared/jars
but it gives ERROR as mentioned below..

##### 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-EYMIaT) does not exist.
##### ERROR 
------------------------------------------------------------------------------------------

Could you please suggest on the same..


Thanks
Sridhar


On Fri, Jul 12, 2013 at 10:17 AM, Ross <ross.laza...@gmail.com> wrote:

> 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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