Hi,

I have recently shifted from GATK 3 to GATK4. It has changed very much. I figured most of the step but one thing is giving me problem is that how to set temporary directory option in GATK4. I have used this option `export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp ` with this option `--TMP_DIR ./tmp/`. As mentioned in [this link][1] But it is giving me this error

    A USER ERROR has occurred: 'export' is not a valid command.

Can any one please tell me how to resolve this error.
  [1]: https://gatkforums.broadinstitute.org/gatk/discussion/comment/46418#Comment_46418
You are probably executing `gatk` as:

    gatk export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp

What you want, probably (and not tested), is:


    export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
    
    gatk <command> <options>

Or just (what I would do):

    gatk <command> <options> --TMP_DIR=./tmp 