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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to