cade13fb56eb21ed057867859814ff02ba55457b
max
  Mon Dec 2 08:51:11 2019 -0800
adding medline info to AVADA track, refs #24156

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index dd97abe..5e2e4ac 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33606,35 +33606,40 @@
             -syntenicNet) > swap.log 2>&1
     #  real    56m29.163s
 
     cat fb.rheMac10.chainHg19Link.txt
     # 2483311773 bases of 2936892733 (84.556%) in intersection
     cat fb.rheMac10.chainSynHg19Link.txt
     # 2461925388 bases of 2936892733 (83.828%) in intersection
 
     time (doRecipBest.pl -workhorse=hgwdev -load -buildDir=`pwd` rheMac10 hg19) > rbest.log 2>&1
     # real    112m15.825s
 
     cat fb.rheMac10.chainRBest.Hg19.txt
     # 2423781773 bases of 2936892733 (82.529%) in intersection
 
 #########################################################################
-# 2019-09-17: AVADA fulltext variants, Max
+# 2019-12-02: AVADA fulltext variants, Max
 cd /hive/data/genomes/hg19/bed/avada
 wget http://bejerano.stanford.edu/AVADA/avada_v1.00_2016.vcf.gz
 python ~/kent/src/hg/makeDb/avada/toBed.py > avada.bed
-bedToBigBed avada.bed /hive/data/genomes/hg19/chrom.sizes -as=${HOME}/kent/src/hg/makeDb/avada/avada.as -tab avada.bb -type=bed9+
+cat avada.bed | sort -k10 > avada.s.bed
+cp /hive/data/inside/pubs/text/medline/articles.db /dev/shm/max/
+bedAppendPaperInfo avada.s.bed avadaPapers.bed  --db /dev/shm/max
+bedSort avadaPapers.bed avadaPapers.bed
+bedToBigBed avadaPapers.bed /hive/data/genomes/hg19/chrom.sizes -as=${HOME}/kent/src/hg/makeDb/avada/avada.as  -tab avada.bb -type=bed9+   
+rm /dev/shm/max/articles.db
 cd /gbdb/hg19/bbi
 ln -s /hive/data/genomes/hg19/bed/avada/avada.bb
 
 #########################################################################
 # Hi-C example track drawing from Rao 2014 - (DONE - 2019-10-07 - Jonathan)
 mkdir -p /hive/data/genomes/hg19/bed/hic
 cd /hive/data/genomes/hg19/bed/hic
 
 # Files are located on GEO at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525.  I grabbed the hic files
 # and used a subset of them (the combined files that haven't been filtered).
 wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_GM12878_insitu_primary%2Breplicate_combined.hic
 wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_HMEC_combined.hic
 wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_HUVEC_combined.hic
 wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_IMR90_combined.hic
 wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_K562_combined.hic