src/hg/utils/automation/makeDownloads.pl 1.23

Index: src/hg/utils/automation/makeDownloads.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/makeDownloads.pl,v
retrieving revision 1.22
retrieving revision 1.23
diff -b -B -U 4 -r1.22 -r1.23
--- src/hg/utils/automation/makeDownloads.pl	8 Jun 2009 18:38:58 -0000	1.22
+++ src/hg/utils/automation/makeDownloads.pl	29 Jul 2009 18:59:18 -0000	1.23
@@ -267,15 +267,17 @@
   my $hgFakeAgpDir = "$HgAutomate::trackBuild/hgFakeAgp";
   my $agpFile = &mustFindOne("$db.agp", 'scaffolds.agp',
 			     "$hgFakeAgpDir/$db.agp",
 			     "$hgFakeAgpDir/scaffolds.agp");
-  my $outFile = &mustFindOne("$db.fa.out", 'scaffolds.out');
+  my $outFile = &mustFindOne("$db.fa.out", 'scaffolds.out', "bed/repeatMasker/$db.fa.out");
   my $trfFile = &mustFindOne("$trfRunDirRel/trfMask.bed",
 			     "$trfRunDirRel/scaffolds.bed");
   $bossScript->add(<<_EOF_
 # Make compressed files of .agp, .out, TRF .bed, soft- and hard-masked .fa:
 cd $runDir/bigZips
 
+ln -s $topDir/$db.2bit ./$db.2bit
+
 gzip -c $agpFile > $db.agp.gz
 gzip -c $outFile > $db.fa.out.gz
 gzip -c $trfFile > $db.trf.bed.gz
 
@@ -630,8 +632,18 @@
   $projectUrl
 
 Files included in this directory:
 
+$db.2bit - contains the complete $organism/$db genome sequence
+    in the 2bit file format.  The utility program, twoBitToFa (available
+    from the kent src tree), can be used to extract .fa file(s) from
+    this file.  A pre-compiled version of the command line tool can be
+    found at:
+        http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
+    See also:
+        http://genome.ucsc.edu/admin/cvs.html
+	http://genome.ucsc.edu/admin/jk-install.html
+
 _EOF_
   ;
   if ($chromBased) {
     print $fh <<_EOF_
@@ -949,10 +961,14 @@
 # Add md5sum.txt and README.txt to each dir:
 foreach d (bigZips $chromGz database liftOver)
   cd $runDir/\$d
   if (\$d != "database" && \$d != "liftOver") then
+    if (-s $db.2bit) then
+	md5sum $db.2bit *.gz > md5sum.txt
+    else
     md5sum *.gz > md5sum.txt
   endif
+  endif
   mv $runDir/README.\$d.txt README.txt
 end
 
 _EOF_