mkdir /cluster/data/hg38/bed/gdcCancer
cd /cluster/data/hg38/bed/gdcCancer

#go to https://portal.gdc.cancer.gov/repository?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.access%22%2C%22value%22%3A%5B%22open%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.analysis.workflow_type%22%2C%22value%22%3A%5B%22MuTect2%20Variant%20Aggregation%20and%20Masking%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_format%22%2C%22value%22%3A%5B%22MAF%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_type%22%2C%22value%22%3A%5B%22Masked%20Somatic%20Mutation%22%5D%7D%7D%5D%7D
# add files to cart, click on cart, hit download button

# press clinical button and select TSV.  Download will contain clinical.tsv exposure.tsv

tar xvf gdc_download_20190408_221221.617568.tar.gz
tar xvf clinical.cart.2019-04-22.tar.gz

cancerMafToBigBed . clinical.tsv exposure.tsv gdcCancer.bb

#rebuild the bb with a polished AS file
bedToBigBed -as=$HOME/kent/src/hg/lib/gdcCancer.as -type=bed12+ -tab gdcCancer.s.bed /cluster/data/hg38/chrom.sizes gdcCancer.bb

rm /gbdb/hg38/gdcCancer.bb
ln -s `pwd`/gdcCancer.bb /gbdb/hg38

for i in */*.maf.gz; do 
dir=`dirname $i`; name=`basename $i | sed 's/TCGA.//' | sed 's/\..*//'`; 
echo cancerMafToBigBed $dir clinical.tsv exposure.tsv $name.bb;
echo bedToBigBed -as=$HOME/kent/src/hg/lib/gdcCancer.as -type=bed12+ -tab $name.s.bed /cluster/data/hg38/chrom.sizes $name.bb
done > jobs

sh -x jobs

for i in *.bb; do ln -s `pwd`/$i /gbdb/hg38/gdcCancer; done

ls */*.maf.gz | while read name; do 
f=`basename $name`; echo $f; done | sort > sortedNames.txt

sum=1
for j in `cat sortedNames.txt`; do 
i=*/$j
dir=`dirname $i`; 
name=`basename $i | sed 's/TCGA.//' | sed 's/\..*//'`; 
sum=`expr $sum + 1`
long=`grep $name project2LongLabel.txt | tawk '{print $2}'`
echo "track $name"
echo "priority $sum"
echo "parent gdcCancer off"
echo "shortLabel $name"
echo "longLabel $long"
echo "group phenDis"
echo "type bigLolly"
echo "lollyField 13"
echo "release alpha"
echo "bigDataUrl /gbdb/hg38/gdcCancer/$name.bb"
echo "autoScale on"
echo "urls case_id=https://portal.gdc.cancer.gov/cases/$$"
echo "genderFilterValues male,female"
echo "genderFilterType multipleListOr"
echo ""
done >> $HOME/kent/src/hg/makeDb/trackDb/human/hg38/gdcCancer.ra