Sridha, There's a difference between your two errors. In the first error for fastqc, Galaxy can't find the source. In the second error, for GATK, the source is being found and executed OK, but GATK is throwing an error ("The fasta file you specified (/tmp/tmp-gatk-EYMIaT) does not exist."). I'm not familiar enough with GATK to know why it's throwing this error. Sorry. Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 12/07/2013 06:52, "sridhar srinivasan" <sridhar2bioinfo@gmail.com> wrote:

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.lazarus@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 <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/d ataset_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