Better handle TCGA sample names in vcf/base.pm
change file format .. earlier format was not formatted corrected for NCBI
No hardcoded path for $ENV{GENOME_TEST_URL}

Updated $ENV{GENOME_TEST_URL} in Site/TGI.pm so it no longer uses a
hardcoded path. It now uses the directory specified by
$ENV{GENOME_TEST_INPUTS}.
Fixed data loss issue when creating allocations

Fixed an issue where data loss could occur when creating allocations. If
the allocation system attempted to create an allocation that had an
absolute path that already existed on the file system (and that path did
not already have an allocation), that path would be deleted when the
allocation system created and soon after deleted a "candidate"
allocation for that path. Creating an allocation now checks for this
condition.
updated gmt copy-number cna-seg to use files in the tgi-misc-annotation file db