026fea8dd26483276dbc4d8c860ff0d11e1a640e
hiram
  Thu Jan 23 15:27:43 2020 -0800
now using new minimal makefile with single set of scripts refs #24748

diff --git src/hg/makeDb/doc/vertebratesAsmHub/mkGenomes.pl src/hg/makeDb/doc/vertebratesAsmHub/mkGenomes.pl
deleted file mode 100755
index ad51cf0..0000000
--- src/hg/makeDb/doc/vertebratesAsmHub/mkGenomes.pl
+++ /dev/null
@@ -1,182 +0,0 @@
-#!/usr/bin/env perl
-
-use strict;
-use warnings;
-use File::Basename;
-
-my %betterName;	# key is asmId, value is common name
-my $hubName = "vertebrate";
-my $srcDocDir = "vertebratesAsmHub";
-my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild";
-my $destDir = "/hive/data/genomes/asmHubs/$hubName";
-
-my $home = $ENV{'HOME'};
-my $srcDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir";
-my $commonNameList = "$hubName.asmId.commonName.tsv";
-my $commonNameOrder = "$hubName.commonName.asmId.orderList.tsv";
-
-
-open (FH, "<$srcDir/${commonNameList}") or die "can not read $srcDir/${commonNameList}";
-while (my $line = <FH>) {
-  chomp $line;
-  my ($asmId, $name) = split('\t', $line);
-  $betterName{$asmId} = $name;
-}
-close (FH);
-
-my @orderList;	# asmId of the assemblies in order from the *.list files
-# the order to read the different .list files:
-my $assemblyCount = 0;
-
-open (FH, "<$srcDir/${commonNameOrder}") or die "can not read ${commonNameOrder}";
-while (my $line = <FH>) {
-  chomp $line;
-  my ($commonName, $asmId) = split('\t', $line);
-  push @orderList, $asmId;
-  ++$assemblyCount;
-}
-close (FH);
-
-my $orderKey = 1;
-foreach my $asmId (reverse(@orderList)) {
-  my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/" . substr($asmId, 0 ,3);
-  $buildDir .= "/" . substr($asmId, 4 ,3);
-  $buildDir .= "/" . substr($asmId, 7 ,3);
-  $buildDir .= "/" . substr($asmId, 10 ,3);
-  $buildDir .= "/" . $asmId;
-  my $asmReport="$buildDir/download/${asmId}_assembly_report.txt";
-  my $descr=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.*organism name: *##i; s# (.*\$##;'`;
-  chomp $descr;
-  my $orgName=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.* name: .* (##; s#).*##;'`;
-  chomp $orgName;
-  $orgName = $betterName{$asmId} if (exists($betterName{$asmId}));
-
-  printf "genome %s\n", $asmId;
-  printf "trackDb genomes/%s/%s.trackDb.txt\n", $asmId, $asmId;
-  printf "groups groups.txt\n";
-  printf "description %s\n", $orgName;
-  printf "twoBitPath genomes/%s/%s.2bit\n", $asmId, $asmId;
-  printf "organism %s\n", $descr;
-  my $chrName=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$1}'`;
-  chomp $chrName;
-  my $bigChrom=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$NF}'`;
-  chomp $bigChrom;
-  my $oneThird = int($bigChrom/3);
-  my $tenK = $oneThird + 10000;
-  $tenK = $bigChrom if ($tenK > $bigChrom);
-  my $defPos="${chrName}:${oneThird}-${tenK}";
-  if ( -s "$asmId/defaultPos.txt" ) {
-    $defPos=`cat "$asmId/defaultPos.txt"`;
-    chomp $defPos;
-  }
-  printf "defaultPos %s\n", $defPos;
-  printf "orderKey %d\n", $orderKey++;
-  printf "scientificName %s\n", $descr;
-  printf "htmlPath genomes/%s/html/%s.description.html\n", $asmId, $asmId;
-  printf "\n";
-  my $localGenomesFile = "$buildDir/${asmId}.genomes.txt";
-  open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile";
-  printf GF "genome %s\n", $asmId;
-  printf GF "trackDb %s.trackDb.txt\n", $asmId;
-  printf GF "groups %s.groups.txt\n", $asmId;
-  printf GF "description %s\n", $orgName;
-  printf GF "twoBitPath %s.2bit\n", $asmId;
-  printf GF "organism %s\n", $descr;
-  printf GF "defaultPos %s\n", $defPos;
-  printf GF "orderKey %d\n", $orderKey++;
-  printf GF "scientificName %s\n", $descr;
-  printf GF "htmlPath html/%s.description.html\n", $asmId;
-  close (GF);
-  my $localHubTxt = "$buildDir/${asmId}.hub.txt";
-  open (HT, ">$localHubTxt") or die "can not write to $localHubTxt";
-  printf HT "hub %s genome assembly\n", $asmId;
-  printf HT "shortLabel %s\n", $orgName;
-  printf HT "longLabel %s/%s/%s genome assembly\n", $orgName, $descr, $asmId;
-  printf HT "genomesFile %s.genomes.txt\n", $asmId;
-  printf HT "email hclawson\@ucsc.edu\n";
-  printf HT "descriptionUrl html/%s.description.html\n", $asmId;
-  close (HT);
-
-  my $localGroups = "$buildDir/${asmId}.groups.txt";
-  open (GR, ">$localGroups") or die "can not write to $localGroups";
-  print GR <<_EOF_
-name user
-label Custom
-priority 1
-defaultIsClosed 1
-
-name map
-label Mapping
-priority 2
-defaultIsClosed 0
-
-name genes
-label Genes
-priority 3
-defaultIsClosed 0
-
-name rna
-label mRNA
-priority 4
-defaultIsClosed 0
-
-name regulation
-label Regulation
-priority 5
-defaultIsClosed 0
-
-name compGeno
-label Comparative
-priority 6
-defaultIsClosed 0
-
-name varRep
-label Variation
-priority 7
-defaultIsClosed 0
-
-name x
-label Experimental
-priority 10
-defaultIsClosed 1
-_EOF_
-   ;
-   close (GR);
-}
-
-__END__
-
-description Mastacembelus armatus
-twoBitPath GCA_900324485.2_fMasArm1.2/trackData/addMask/GCA_900324485.2_fMasArm1.2.masked.2bit
-organism Zig-Zag eel
-defaultPos LR535842.1:14552035-14572034
-orderKey 1
-scientificName Mastacembelus armatus
-htmlPath GCA_900324485.2_fMasArm1.2/html/GCA_900324485.2_fMasArm1.2.description.html
-
-# head -25 GCA_002180035.3_HG00514_prelim_3.0_assembly_report.txt
-
-# Assembly name:  HG00514_prelim_3.0
-# Organism name:  Homo sapiens (human)
-# Isolate:  HG00514
-# Sex:  female
-# Taxid:          9606
-# BioSample:      SAMN04229552
-# BioProject:     PRJNA300843
-# Submitter:      The Genome Institute at Washington University School of Medicine
-# Date:           2018-05-22
-# Assembly type:  haploid
-# Release type:   major
-# Assembly level: Chromosome
-# Genome representation: full
-# WGS project:    NIOH01
-# Assembly method: Falcon v. November 2016
-# Expected final version: no
-# Genome coverage: 80.0x
-# Sequencing technology: PacBio RSII
-# GenBank assembly accession: GCA_002180035.3
-#
-## Assembly-Units:
-## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
-## GCA_002180045.3              Primary Assembly
-