src/hg/archaeStuff/scripts/make-browser-2.0 1.44

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 1.43
retrieving revision 1.44
diff -b -B -U 4 -r1.43 -r1.44
--- src/hg/archaeStuff/scripts/make-browser-2.0	2 Aug 2009 05:07:15 -0000	1.43
+++ src/hg/archaeStuff/scripts/make-browser-2.0	3 Aug 2009 20:32:51 -0000	1.44
@@ -72,9 +72,9 @@
 
 # Program option variables
 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_igenics,
- $opt_syncg,$opt_synct,$opt_syncd, $opt_syncc, $opt_syncdw, $opt_loaddump, $opt_allorg,$opt_snapshot,
+ $opt_syncg,$opt_synct,$opt_syncd, $opt_syncc, $opt_syncdw, $opt_loaddump, $opt_allorg,$opt_snapshot, $opt_cleanblast,
  $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,
  $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,
@@ -144,8 +144,9 @@
         next;
     }
 
     if ($opt_loaddump)             { &Load_dbdump(\%global_vars); &Load_desc_page(\%global_vars); }
+    if ($opt_cleanblast)           { &Clean_blast_hits(\%global_vars); }
     if ($opt_initdb)               { &Initialize_org_db(\%global_vars); }
     if ($opt_syncg)                { &Sync_genome_db(\%global_vars, "public"); }
     if ($opt_synct)                { &Sync_genome_db(\%global_vars, "test"); }
     if ($opt_syncd)                { &Sync_genome_db(\%global_vars, "dev"); }
@@ -383,9 +384,9 @@
     $opt_auth = '';
     $opt_precomp = '';
     $opt_swissprot = '';
 
-    Getopt::Long::GetOptions("getseqs","joinassembly", "initdb","hidedb","droptable=s","initblat","gc","gbhits",
+    Getopt::Long::GetOptions("getseqs","joinassembly", "initdb","hidedb","droptable=s","initblat","gc","gbhits","cleanblast",
                  "repeats","iselements", "desc","info",
                  "pfam","scanpfam",
                  "genes","genepred","cogs","kegg","gbrnas","trnas","snornas","delete=s", "igenics",
                  "syncg","synct","syncd","syncc","syncdw","loaddump", "swissprot=s", "pfamdesc",
@@ -433,8 +434,9 @@
     "            --commit  :  cvs commit changes to description.html front page\n",
     "            --perm    :  Set permissions to group-writeable for all files\n",
     "            --public  :  Required to update public genome server DB\n",
     "            --loaddump:  Load mySql database for organism onto current server (after running --syncg command)\n",
+    "            --cleanblast:  Clean blast hits to genomes that do not exist in centraldb\n",
     "            --web=<file>  :  Print web links and image map info using coordinates from <file>\n",
     "            --snapshot <browser addr> :  Save an image snapshot of <browser addr> (i.e. archaea.ucsc.edu)\n",
     "            --auth <user:pass>        :  Used with --snapshot to authorize access to protected sites\n\n",