src/hg/archaeStuff/scripts/make-browser-2.0 1.37

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 1.36
retrieving revision 1.37
diff -b -B -U 4 -r1.36 -r1.37
--- src/hg/archaeStuff/scripts/make-browser-2.0	20 Mar 2009 19:09:43 -0000	1.36
+++ src/hg/archaeStuff/scripts/make-browser-2.0	31 Mar 2009 06:57:20 -0000	1.37
@@ -98,9 +98,9 @@
 our @promsd_wig_names = ("promoterScanPos","promoterScanNeg","shineDGPos","shineDGNeg");
 
 
 # Program option variables
-our ($opt_getseqs, $opt_initdb, $opt_hidedb, $opt_droptable, $opt_initblat, $opt_gc, $opt_repeats, $opt_iselements,
+our ($opt_getseqs, $opt_joinassembly, $opt_initdb, $opt_hidedb, $opt_droptable, $opt_initblat, $opt_gc, $opt_repeats, $opt_iselements,
  $opt_desc, $opt_info, $opt_pfam, $opt_scanpfam, $opt_swissprot, $opt_pfamdesc,
  $opt_syncg,$opt_synct,$opt_syncd, $opt_syncc, $opt_loaddump, $opt_allorg,$opt_snapshot,
  $opt_genes, $opt_gbhits, $opt_genepred, $opt_cogs, $opt_kegg, $opt_gbrnas, $opt_trnas, $opt_snornas,$opt_auth,
  $opt_rfam, $opt_tigr, $opt_jgi, $opt_easy, $opt_startblat, $opt_killblat, $opt_blatscript, $opt_selfz, $opt_multiz, $opt_ultracons,
@@ -119,8 +119,9 @@
 
 # Main
 &Read_genome_info($global_constants->genome_info(), \%global_vars);       # default genome information
 &Read_genome_info($global_constants->genome_info_vir(), \%global_vars);   # default genome information for viruses
+&Read_genome_info($global_constants->genome_info_meta(), \%global_vars);  # metagenome information
 &Read_genome_info($global_constants->genome_info_mods(), \%global_vars);  # manual changes to genome info
 &Read_genome_info($global_constants->genome_info_euk(), \%global_vars);   # manual genome information for eukaryotes
 
 &Check_supported_org_list(\%org_abbr_AR,                                  # check support org list for typo's
@@ -160,8 +161,9 @@
     $utils->org_name($organism->org_name());
 
     if ($opt_info)                 { $organism->Print_org_info($global_constants->gbdb_dir(), $global_constants->Supported_organisms());  }
     if ($opt_getseqs)              { &Copy_seqs(\%global_vars); }
+    if ($opt_joinassembly)         { &Join_assemblies(\%global_vars); }
     if ($opt_hidedb)               { &Hide_org_db(\%global_vars); }
     if ($opt_droptable ne '')      { &Drop_org_table(\%global_vars, $opt_droptable); }
 
     if (!-d $global_constants->cluster_data_dir()."/".$organism->db_name())
@@ -411,9 +413,9 @@
     $opt_auth = '';
     $opt_precomp = '';
     $opt_swissprot = '';
 
-    Getopt::Long::GetOptions("getseqs","initdb","hidedb","droptable=s","initblat","gc","gbhits",
+    Getopt::Long::GetOptions("getseqs","joinassembly", "initdb","hidedb","droptable=s","initblat","gc","gbhits",
                  "repeats","iselements", "desc","info",
                  "pfam","scanpfam",
                  "genes","genepred","cogs","kegg","gbrnas","trnas","snornas","delete=s",
                  "syncg","synct","syncd","syncc","loaddump", "swissprot=s", "pfamdesc",
@@ -439,8 +441,9 @@
 
     "   DATABASE & FILE MAINTENANCE\n",
     "            --info      :  Print information about selected species in Genome-info-db/mods files\n",
     "            --getseqs   :  Get & format genome sequence files \n",
+    "            --joinassembly   :  Format multiple-scaffold assemblies as a single genome \n",
     "            --initdb    :  Initialize organism database\n",
     "            --desc      :  Create basic description.html page (must run --genes first)\n",
     "            --hidedb    :  Delete organism from menu (but not data)\n",
     "            --droptable=<table> : Drop <table> from organism\n",