src/hg/archaeStuff/scripts/make-browser-2.0 1.53

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 1.52
retrieving revision 1.53
diff -b -B -U 4 -r1.52 -r1.53
--- src/hg/archaeStuff/scripts/make-browser-2.0	20 Jan 2010 23:03:34 -0000	1.52
+++ src/hg/archaeStuff/scripts/make-browser-2.0	21 Mar 2010 01:00:05 -0000	1.53
@@ -35,8 +35,9 @@
 use archaeBrowser::RNAStructure;
 use archaeBrowser::Annotation;
 use archaeBrowser::AlignmentCompare;
 use archaeBrowser::CRISPR;
+use archaeBrowser::Phylo;
 
 
 # Global constants
 our $global_constants = archaeBrowser::Constant->new;
@@ -81,9 +82,9 @@
  $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_trnablat, $opt_annotrev, $opt_crispr);
+ $opt_predictGenes, $opt_rrnablat, $opt_trnablat, $opt_annotrev, $opt_crispr, $opt_genetree);
 
 
 
 # By default, we are not looking for any particular organism to start our work
@@ -211,8 +212,9 @@
     if ($opt_mblastxall)           { &Load_mBlastX_track(\%global_vars,"full-rescan", 0);  }
     if ($opt_predictGenes)         { &PredictGenes(\%global_vars);   }
     if ($opt_annotrev ne '')       { &Load_annotation_revision(\%global_vars, $opt_annotrev); }
     if ($opt_crispr)               { &Load_CRISPRs(\%global_vars);   }
+    if ($opt_genetree)             { &Load_gene_tree(\%global_vars);  }
     if ($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);   }
@@ -413,9 +415,9 @@
                  "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", "trnablat", "annotrev=s", "crispr");
+                 "cdd", "aligntracks", "predictGenes", "rrnablat", "trnablat", "annotrev=s", "crispr", "genetree");
 
     if ($#ARGV < 0)
     {
     die "\nUsage: make-browser [-options] <Org-ident>\n\n",
@@ -465,8 +467,9 @@
     "            --all     :  Create/Load/Run all tasks (does not set --force)\n",
     "            --gc        :  Run G/C percent track\n",
     "            --repeats   :  Run simple repeats\n",
     "            --genes     :  Load primary gene track (i.e. Genbank Refseq or other)\n",
+    "            --genetree  :  Load gene trees (must be run after --genes and --blastp)\n",
     "            --annotrev=<release date> : Load revised annotation track\n",
     "            --igenics   :  Load intergenic regions between CDS\n",
     "            --gbhits    :  Map sequenced genes & cDNAs in Genbank to genome\n",
     "            --promsd    :  Load precomputed promotor & Shine-Dalgarno tracks, if present\n",