435fbceebeaddec93ebca4eaa50b20123967a285
angie
  Fri Oct 25 11:40:25 2019 -0700
LRG: if source URL is missing a protocol, prepend http:// .  Thx Jairo.  refs #24285

diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt
index 2890bc5..36a733a 100644
--- src/hg/makeDb/doc/hg38/hg38.txt
+++ src/hg/makeDb/doc/hg38/hg38.txt
@@ -3633,31 +3633,31 @@
     time (doBlastzChainNet.pl -verbose=2 \
         /hive/data/genomes/hg38/bed/lastzMonDom5.2014-05-27/DEF \
         -swap -chainMinScore=5000 -chainLinearGap=loose \
         -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
         -syntenicNet) > swap.log 2>&1
     # real    102m41.443s
 
     cat fb.monDom5.chainHg38Link.txt
     # 420069915 bases of 3501660299 (11.996%) in intersection
     time (/cluster/bin/scripts/doRecipBest.pl -buildDir=`pwd` \
         -dbHost=hgwdev -workhorse=hgwdev monDom5 hg38) > rbest.log 2>&1
     #  real    90m56.189s
 
 _EOF_
 #############################################################################
-# LOCUS REFERENCE GENOMIC (LRG) REGIONS AND TRANSCRIPTS (DONE 10/9/19 angie)
+# LOCUS REFERENCE GENOMIC (LRG) REGIONS AND TRANSCRIPTS (DONE 10/25/19 angie)
 # Redmine #13359, #24285 -- otto-mate To Do #17877
 # previously done 7/7/14, 9/9/16, 5/30/18
     set today = `date +%Y_%m_%d`
     mkdir -p /hive/data/genomes/hg38/bed/lrg/$today
     cd /hive/data/genomes/hg38/bed/lrg/$today
     wget ftp://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_public_xml_files.zip
     unzip LRG_public_xml_files.zip
 
     # Run script to convert LRG*.xml files to BED+ for regions and genePredExt+fa for transcripts:
     ~/kent/src/hg/utils/automation/parseLrgXml.pl GRCh38
     genePredCheck lrgTranscriptsUnmapped.gp
 #Error: lrgTranscriptsUnmapped.gp:765: LRG_7t1 no exonFrame on CDS exon 46
 #checked: 1029 failed: 1
     # If there are complaints e.g. about exonFrame, look for inconsistencies in the
     # affected transcript's coding_region/coordinates vs. exon/intron info in xml.