src/hg/archaeStuff/scripts/make-browser-2.0 1.48

Index: src/hg/archaeStuff/scripts/make-browser-2.0
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/scripts/make-browser-2.0,v
retrieving revision 1.47
retrieving revision 1.48
diff -b -B -U 4 -r1.47 -r1.48
--- src/hg/archaeStuff/scripts/make-browser-2.0	21 Sep 2009 07:31:49 -0000	1.47
+++ src/hg/archaeStuff/scripts/make-browser-2.0	22 Sep 2009 22:07:50 -0000	1.48
@@ -79,9 +79,9 @@
  $opt_plfold, $opt_pldensity, $opt_custwig, $opt_wiki, $opt_wikibme, $opt_promsd, $opt_term, $opt_stringdb,
  $opt_arkops, $opt_tigrops, $opt_commit, $opt_perm, $opt_tracksup, $opt_altdb, $opt_primers,
  $opt_precomp, $opt_blastp, $opt_force, $opt_delete,$opt_web, $opt_public, $opt_all,
  $opt_makeblastdb, $opt_pubmultiz, $opt_cdd, $opt_blastpall, $opt_blastx, $opt_blastxall, $opt_mblastx, $opt_mblastxall, $opt_aligntracks,
- $opt_predictGenes, $opt_rrnablat);
+ $opt_predictGenes, $opt_rrnablat, $opt_trnablat);
 
 
 
 # By default, we are not looking for any particular organism to start our work
@@ -177,8 +177,9 @@
     if ($opt_trnas || $opt_all)    { &Load_tRNA_track(\%global_vars);   }
     if ($opt_snornas)              { &Load_snoRNA_track(\%global_vars); }
     if ($opt_rfam || $opt_all)     { &Load_RFAM_track(\%global_vars);   }
     if ($opt_rrnablat)             { &Load_rRNA_Blat_track(\%global_vars); }
+    if ($opt_trnablat)             { &Load_tRNA_Blat_track(\%global_vars); }
     if ($opt_tigr)                 { &Load_TIGR_gene_track(\%global_vars);     }
     if ($opt_jgi || $opt_all)      { &Load_JGI_gene_track(\%global_vars);      }
     if ($opt_stringdb || $opt_all) { &Load_StringDb_track(\%global_vars);      }
     if ($opt_easy || $opt_all)     { &Load_Easygene_track(\%global_vars);      }
@@ -407,9 +408,9 @@
                  "stringdb",
                  "plfold","pldensity","custwig=s","wiki", "wikibme","promsd","term","arkops","tigrops","auth=s",
                  "commit","perm","tracksup","altdb=s","primers","precomp=s","snapshot=s",
                  "blastp","blastpall","blastx","blastxall","mblastx","mblastxall","force","web=s","public","all","allorg","makeblastdb", "pubmultiz",
-                 "cdd", "aligntracks", "predictGenes", "rrnablat");
+                 "cdd", "aligntracks", "predictGenes", "rrnablat", "trnablat");
 
     if ($#ARGV < 0)
     {
     die "\nUsage: make-browser [-options] <Org-ident>\n\n",
@@ -473,8 +474,9 @@
     "            --trna    :  Load tRNAscan-SE track\n",
     "            --snorna  :  Load C/D guide snoRNAs track\n",
     "            --rfam    :  Load Rfam track\n",
     "            --rrnablat :  Load rRNA Blat hit track\n",
+    "            --trnablat :  Load tRNA Blat hit track\n",
     "            --tigr    :  Load TIGR genes track\n",
     "            --jgi     :  Load JGI genes track\n",
     "            --easy    :  Load Krogh lab's EasyGene track\n",
     "            --predictGenes : Run Glimmer, GeneMark, and Prodigal gene finders\n",