6c8734919a8bbcc7b0ef17a89ef86d21d80686cb
hiram
  Thu Jan 23 14:25:13 2020 -0800
now using a minimal makefile and common scripts to make any assembly hub refs #24748

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
new file mode 100755
index 0000000..b9dcb81
--- /dev/null
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -0,0 +1,90 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+
+my $argc = scalar(@ARGV);
+if ($argc != 2) {
+  printf STDERR "mkSymLinks Name asmName\n";
+  printf STDERR "e.g.: mkAsmStats Mammals mammals\n";
+  exit 255;
+}
+my $Name = shift;
+my $asmHubName = shift;
+
+my %betterName;	# key is asmId, value is common name
+my $srcDocDir = "${asmHubName}AsmHub";
+
+my $home = $ENV{'HOME'};
+my $srcDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir";
+my $commonNameList = "$asmHubName.asmId.commonName.tsv";
+my $commonNameOrder = "$asmHubName.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 $destDir = "/hive/data/genomes/asmHubs";
+
+my $orderKey = 1;
+foreach my $asmId (reverse(@orderList)) {
+  my $accessionDir = substr($asmId, 0 ,3);
+  $accessionDir .= "/" . substr($asmId, 4 ,3);
+  $accessionDir .= "/" . substr($asmId, 7 ,3);
+  $accessionDir .= "/" . substr($asmId, 10 ,3);
+  $accessionDir .= "/" . $asmId;
+  $destDir = "/hive/data/genomes/asmHubs/$accessionDir";
+  my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir";
+  if ( ! -d "${destDir}" ) {
+    `mkdir -p "${destDir}"`;
+  }
+  printf STDERR "ln -s '${buildDir}' '${destDir}'\n";
+  `rm -f "${destDir}/bbi"`;
+  `rm -f "${destDir}/ixIxx"`;
+  `rm -fr "${destDir}/html"`;
+  `mkdir -p "${destDir}/html"`;
+  `rm -f "${destDir}/${asmId}.2bit"`;
+  `rm -f "${destDir}/${asmId}.agp.gz"`;
+  `rm -f "${destDir}/${asmId}.chrom.sizes"`;
+  `rm -f "${destDir}/${asmId}_assembly_report.txt"`;
+  `rm -f "${destDir}/${asmId}.trackDb.txt"`;
+  `rm -f "${destDir}/${asmId}.genomes.txt"`;
+  `rm -f "${destDir}/${asmId}.hub.txt"`;
+  `rm -f "${destDir}/${asmId}.groups.txt"`;
+  `ln -s "${buildDir}/bbi" "${destDir}/bbi"`;
+  `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"`;
+  `ln -s ${buildDir}/html/*.html "${destDir}/html/"`;
+   my $jpgFiles =`ls ${buildDir}/html/*.jpg 2> /dev/null | wc -l`;
+   chomp $jpgFiles;
+   if ($jpgFiles > 0) {
+    `rm -f ${destDir}/html/*.jpg`;
+    `ln -s ${buildDir}/html/*.jpg "${destDir}/html/"`;
+   }
+#  `ln -s ${buildDir}/html/*.png "${destDir}/genomes/${asmId}/html/"`;
+  `ln -s "${buildDir}/${asmId}.2bit" "${destDir}/"`;
+  `ln -s "${buildDir}/${asmId}.agp.gz" "${destDir}/"`;
+  `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/"`;
+  `ln -s "${buildDir}/download/${asmId}_assembly_report.txt" "${destDir}/"`;
+  `ln -s "${buildDir}/${asmId}.trackDb.txt" "${destDir}/"`;
+  `ln -s "${buildDir}/${asmId}.genomes.txt" "${destDir}/"`;
+  `ln -s "${buildDir}/${asmId}.hub.txt" "${destDir}/"`;
+  `ln -s "${buildDir}/${asmId}.groups.txt" "${destDir}/"`;
+}