src/hg/archaeStuff/scripts/make-browser-2.0 1.46

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 1.45
retrieving revision 1.46
diff -b -B -U 4 -r1.45 -r1.46
--- src/hg/archaeStuff/scripts/make-browser-2.0	14 Aug 2009 17:31:02 -0000	1.45
+++ src/hg/archaeStuff/scripts/make-browser-2.0	20 Sep 2009 23:58:28 -0000	1.46
@@ -78,9 +78,10 @@
  $opt_rfam, $opt_tigr, $opt_jgi, $opt_easy, $opt_startblat, $opt_killblat, $opt_blatscript, $opt_selfz, $opt_multiz, $opt_ultracons,
  $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_makeblastdb, $opt_pubmultiz, $opt_cdd, $opt_blastpall, $opt_blastx, $opt_blastxall, $opt_mblastx, $opt_mblastxall, $opt_aligntracks,
+ $opt_predictGenes);
 
 
 
 # By default, we are not looking for any particular organism to start our work
@@ -203,8 +204,9 @@
     if ($opt_blastx)               { &Load_igenics(\%global_vars); &Load_BlastX_track(\%global_vars,"incremental");   }
     if ($opt_blastxall)            { &Load_igenics(\%global_vars); &Load_BlastX_track(\%global_vars,"full-rescan");   }
     if ($opt_mblastx)              { &Load_mBlastX_track(\%global_vars,"incremental");   }
     if ($opt_mblastxall)           { &Load_mBlastX_track(\%global_vars,"full-rescan");   }
+    if ($opt_predictGenes)         { &PredictGenes(\%global_vars);   }
     if ($opt_commit || $opt_all)   { &CVS_commit(\%global_vars);        }
     if ($opt_tracksup || $opt_all) { &Update_tracks(\%global_vars);     }
     if ($global_constants->Web_links_file() ne '')     { &Print_web_links($organism);   }
     if ($opt_perm)                 { &Set_permissions(\%global_vars);   }
@@ -282,8 +284,9 @@
 
                 elsif ($org->tax_ID() =~ / $tax_name_key[\;\.]/)
                 {
                     if (($org->tax_ID() =~ / Archaea;/) ||
+                        ($org->tax_ID() =~ / Metagenome./) ||
 			($org->tax_ID() =~ / Viruses;/) ||
 			$opt_allorg ||
                         ((defined $global_constants->Supported_organisms()->{$org->db_name()})))
                     {
@@ -346,8 +349,16 @@
         {
             print "$org_abbr ";
         }
     }
+    print "\nMetagenome:\n";
+    foreach $org_abbr (sort keys(%organism_AR))
+    {
+        if ($organism_AR{$org_abbr}->org_domain() eq "Metagenome")
+        {
+            print "$org_abbr ";
+        }
+    }
     print("\n\n");
 }
 
 sub Read_web_links_info {
@@ -394,9 +405,10 @@
                  "rfam","tigr","jgi","easy","startblat","killblat","blatscript","selfz","multiz", "ultracons",
                  "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");
+                 "blastp","blastpall","blastx","blastxall","mblastx","mblastxall","force","web=s","public","all","allorg","makeblastdb", "pubmultiz",
+                 "cdd", "aligntracks", "predictGenes");
 
     if ($#ARGV < 0)
     {
     die "\nUsage: make-browser [-options] <Org-ident>\n\n",
@@ -462,8 +474,9 @@
     "            --rfam    :  Load Rfam 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",
     "            --blastp  :  Run blastp on all unscanned species' proteins\n",
     "            --blastpall :  Run blastp on ALL species' proteins (slow!)\n",
     "            --blastx  :  Run blastx on all unscanned species' proteins for intergenic regions between proteins\n",
     "            --blastxall :  Run blastx on All species' proteins for intergenic regions between proteins\n",