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I am new to GATK, trying to build Picard because I apparently will need to build Picard sequence directories for my genomes of interest.
I have installed Java6, Java8, ant, and HTSJDK. I have downloaded Picard 2a49ee2.
Following instructions at broadinstitute.github.io/picard/building.html, I have defined JAVA6_HOME, cd'd into broadinstitute-picard-2a49ee2, and when I run ant -lib lib/ant package-commands I get this message (relevant part only)
"BUILD FAILED ... Basedir .../broadinstitute-picard-2a49ee2/htsjdk does not exist"
So it seems I need to do something for the build to know where my HTSJDK lives. Or did my download fail? Am I supposed to make a symbolic link from .../broadinstitute-picard-2a49ee2/htsjdk over to someplace in my HTSJDK directory? If so, to where?
Thanks for any help,