src/hg/archaeStuff/scripts/make-browser-2.0 1.41

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 1.40
retrieving revision 1.41
diff -b -B -U 4 -r1.40 -r1.41
--- src/hg/archaeStuff/scripts/make-browser-2.0	28 Apr 2009 10:55:24 -0000	1.40
+++ src/hg/archaeStuff/scripts/make-browser-2.0	3 May 2009 04:44:56 -0000	1.41
@@ -78,9 +78,9 @@
  $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_aligntracks);
+ $opt_makeblastdb, $opt_pubmultiz, $opt_cdd, $opt_blastpall, $opt_mblastx, $opt_mblastxall, $opt_aligntracks);
 
 
 
 # By default, we are not looking for any particular organism to start our work
@@ -195,8 +195,10 @@
     if ($opt_aligntracks)          { &Load_align_genes_track(\%global_vars);   }
     if ($opt_cdd)                  { &Load_Conserved_Domains(\%global_vars)   }
     if ($opt_blastp)               { &Load_BlastP_track(\%global_vars,"incremental");   }
     if ($opt_blastpall)            { &Load_BlastP_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_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);   }
@@ -386,9 +388,9 @@
                  "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","force","web=s","public","all","allorg","makeblastdb", "pubmultiz", "cdd", "aligntracks");
+                 "blastp","blastpall","mblastx","mblastxall","force","web=s","public","all","allorg","makeblastdb", "pubmultiz", "cdd", "aligntracks");
 
     if ($#ARGV < 0)
     {
     die "\nUsage: make-browser [-options] <Org-ident>\n\n",
@@ -453,8 +455,10 @@
     "            --jgi     :  Load JGI genes track\n",
     "            --easy    :  Load Krogh lab's EasyGene track\n",
     "            --blastp  :  Run blastp on all unscanned species' proteins\n",
     "            --blastpall :  Run blastp on ALL species' proteins (slow!)\n",
+    "            --mblastx  :  Run blastx on all unscanned species' proteins for metagenomes with concatenated scaffolds\n",
+    "            --mblastxall  :  Run blastx on All species' proteins for metagenomes with concatenated scaffolds\n",
     "            --primers :  Load available primer tracks\n",
     "            --arkops  :   Load operon info from Arkin microbesonline database\n",
     "            --tigrops :   Load operon info from OperonDB (TIGR)\n",
     "            --stringdb:   Load String DB links track (from EMBL)\n",