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delete tmp files from gatk in local galaxy installation

I am trying to run Haplotype Caller from a local installation of Galaxy. After running it the first time, I changed the env.sh so it could find the .jar file for GATK. Now when I try to run it, I get the following error. I cannot locate the tmp directory to delete the file, and I don't know how to specify a different output file through Galaxy. Any help?

[Wed Jan 22 23:07:26 CST 2014] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/tmp-gatk-0WHp_x/gatk_input.fasta OUTPUT=/tmp/tmp-gatk-0WHp_x/dict2435252299968971001.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Jan 22 23:07:26 CST 2014] Executing as [email protected] on Linux 3.5.0-44-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_25-b30; Picard version: null
[Wed Jan 22 23:07:26 CST 2014] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
FAQ: http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.4-7-g5e89f01):
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 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 MESSAGE: Index file /tmp/tmp-gatk-0WHp_x/gatk_input.dict does not exist but could not be created because: . /tmp/tmp-gatk-0WHp_x/dict2435252299968971001.tmp already exists. Delete this file and try again, or specify a different output file.
ERROR ------------------------------------------------------------------------------------------


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