src/hg/utils/automation/makeGenomeDb.pl 1.28

Index: src/hg/utils/automation/makeGenomeDb.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/makeGenomeDb.pl,v
retrieving revision 1.27
retrieving revision 1.28
diff -b -B -U 4 -r1.27 -r1.28
--- src/hg/utils/automation/makeGenomeDb.pl	5 Feb 2010 23:52:29 -0000	1.27
+++ src/hg/utils/automation/makeGenomeDb.pl	19 Feb 2010 23:15:51 -0000	1.28
@@ -78,9 +78,15 @@
   - The month and year in which this assembly was released by the sequencing
     center.
 
 assemblyLabel XXXXXX
-  - The sequencing center's label or version identifier for this release.
+  - The detailed/long form of the sequencing center's label or version
+    identifier for this release (e.g. 'Genome Center at Washington University,
+    St. Louis, Genus_species 1.2.3').
+
+assemblyShortLabel XXXXXX
+  - The abbreviated form of the sequencing center's label or version identifier
+    for this release (e.g. 'WUGSC 1.2.3').
 
 orderKey NN
   - A priority number (for the central database's dbDb.orderKey column)
     that will determine db's relative position in the assembly menu.
@@ -178,9 +184,9 @@
     $opt_noGoldGapSplit
     /;
 
 # Required config parameters:
-my ($db, $scientificName, $assemblyDate, $assemblyLabel, $orderKey,
+my ($db, $scientificName, $assemblyDate, $assemblyLabel, $assemblyShortLabel, $orderKey,
     $mitoAcc, $fastaFiles, $dbDbSpeciesDir, $taxId);
 # Conditionally required config parameters:
 my ($fakeAgpMinContigGap, $fakeAgpMinScaffoldGap,
     $clade, $genomeCladePriority);
@@ -247,8 +253,9 @@
   $db = &requireVar('db', \%config);
   $scientificName = &requireVar('scientificName', \%config);
   $assemblyDate = &requireVar('assemblyDate', \%config);
   $assemblyLabel = &requireVar('assemblyLabel', \%config);
+  $assemblyShortLabel = &requireVar('assemblyShortLabel', \%config);
   $orderKey = &requireVar('orderKey', \%config);
   $mitoAcc = &requireVar('mitoAcc', \%config);
   $fastaFiles = &requireVar('fastaFiles', \%config);
   $dbDbSpeciesDir = &requireVar('dbDbSpeciesDir', \%config);
@@ -389,9 +396,9 @@
 
   my $acat = "cat";
   my $fcat = "cat";
   my $sli = "";
-  if ($subsetLittleIds eq "Y") {
+  if (defined $subsetLittleIds && $subsetLittleIds eq "Y") {
     $sli = "-1 ";  
   }
   foreach my $file (`ls $fastaFiles 2> /dev/null`) {
     if ($file =~ m/\.gz$/) {
@@ -839,9 +846,9 @@
     (name, description, nibPath, organism,
      defaultPos, active, orderKey, genome, scientificName,
      htmlPath, hgNearOk, hgPbOk, sourceName, taxId)
 VALUES
-    ("$db", "$assemblyDate", "$HgAutomate::gbdb/$db", "$genome",
+    ("$db", "$assemblyDate ($assemblyShortLabel/$db)", "$HgAutomate::gbdb/$db", "$genome",
      "$defaultPos", 1, $orderKey, "$genome", "$scientificName",
      "$HgAutomate::gbdb/$db/html/description.html", 0, 0, "$assemblyLabel",
     $taxId);
 _EOF_
@@ -1072,12 +1079,15 @@
   }
   close($fh);
 
   $fh = &HgAutomate::mustOpen(">$topDir/html/gap.html");
+  my $em = $commonName ? "" : "<em>";
+  my $noEm = $commonName ? "" : "</em>";
   if ($gotAgp) {
     print $fh <<_EOF_
 <H2>Description</H2>
-This track depicts gaps in the assembly.
+This track depicts gaps in the draft assembly ($assemblyDate, $assemblyLabel)
+of the $em\$organism$noEm genome.
 
   *** Developer: remove this statement if no future assemblies are expected:
 
 Many of these gaps &mdash; with the
@@ -1142,9 +1152,10 @@
     ;
   } else {
     print $fh <<_EOF_
 <H2>Description</H2>
-This track depicts gaps in the assembly.
+This track depicts gaps in the draft assembly ($assemblyDate, $assemblyLabel)
+of the $em\$organism$noEm genome.
 
   *** Developer: remove this statement if no future assemblies are expected:
 
 Many of these gaps &mdash; with the
@@ -1183,15 +1194,14 @@
   }
   close($fh);
 
   $fh = &HgAutomate::mustOpen(">$topDir/html/gold.html");
-  my $em = $commonName ? "" : "<em>";
-  my $noEm = $commonName ? "" : "</em>";
   if ($gotAgp) {
     print $fh <<_EOF_
 <H2>Description</H2>
 <P>
-This track shows the draft assembly of the $em\$organism$noEm genome.  
+This track shows the draft assembly ($assemblyDate, $assemblyLabel)
+of the $em\$organism$noEm genome.
 
   *** Developer: check if this is accurate:
 
 Whole-genome shotgun reads were assembled into contigs.  When possible, 
@@ -1215,9 +1225,10 @@
   } else {
     print $fh <<_EOF_
 <H2>Description</H2>
 <P>
-This track shows the draft assembly of the $em\$organism$noEm genome.  
+This track shows the draft assembly ($assemblyDate, $assemblyLabel)
+of the $em\$organism$noEm genome.
 
   *** Developer: check if this is accurate:
 
 Whole-genome shotgun reads were assembled into contigs.  When possible,