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This may be a transient problem, but I've been consistently getting corrupted downloads of GATK2 this afternoon. It looks like a php warning gets tacked onto the front:
$ head -c 490 GenomeAnalysisTK-2.0-21.tar.bz2 <br /> <b>Warning</b>: date(): It is not safe to rely on the system's timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected the timezone 'UTC' for now, but please set date.timezone to select your timezone. in <b>/local/software/apache2/htdocs/gatk/auth.php</b> on line <b>43</b><br /> $
But just stripping these bytes isn't quite sufficient to extract it