33c5e452f2df131473468f0206a360a16ba9dcd3
hiram
  Tue Oct 27 13:15:17 2020 -0700
update per alert from Terence for new versions although hg19 needs to wait for the new files refs #26428

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index d5ad7a5..82ab2a2 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33769,16 +33769,31 @@
 mkdir run
 seq 4 57 | parallel -j10 'zcat all.baselevel.021620.tsv.bgz | cut -f1-3,{} | gzip -c > run/tissue{}.pext.gz'
 
 # overlapping exons in coding regions causes problems, don't output any scores
 # for those regions
 seq 4 57 | parallel --joblog run.log -j20 './buildPext.py run/tissue{}.pext.gz -o split'
 tail -n +2 run.log | cut -f4 | awk '{sum += $1}END{print sum/NR}'
 452.034
 
 # Turn into bigWigs:
 find split/ -name "*.bed" | parallel -j15 'sort -k1,1 -k2,2n {} | cut -f1-3,5 > {.}.bedGraph'
 find split/ -name "*.bedGraph" | parallel -j15 'bedGraphToBigWig {} /hive/data/genomes/hg19/chrom.sizes {.}.bw'
 mkdir -p /gbdb/hg19/gnomAD/pext
 ln -s `pwd`/split/*.bw /gbdb/hg19/gnomAD/pext/
 
+#############################################################################
+# update 2020-10-27 (DONE - Hiram - 2020-10-27)
+
+  mkdir /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2020-10-27
+  cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2020-10-27
+
+  time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
+      -bigClusterHub=ku -dbHost=hgwdev \
+      -fileServer=hgwdev -smallClusterHub=hgwdev -workhorse=hgwdev \
+      GCF_000001405.25_GRCh37.p13 hg19) > do.log 2>&1 &
+  # real    6m47.005s
+
+  cat fb.ncbiRefSeq.hg19.txt
+  # 93720294 bases of 2991710746 (3.133%) in intersection
 
+#############################################################################