src/hg/archaeStuff/scripts/make-browser-2.0 1.55
1.55 2010/04/18 20:52:46 pchan
add resetorder, synctable, and synctrackfile options
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 1.54
retrieving revision 1.55
diff -b -B -U 4 -r1.54 -r1.55
--- src/hg/archaeStuff/scripts/make-browser-2.0 22 Mar 2010 04:17:48 -0000 1.54
+++ src/hg/archaeStuff/scripts/make-browser-2.0 18 Apr 2010 20:52:46 -0000 1.55
@@ -75,9 +75,10 @@
# 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_generefs,
- $opt_syncg,$opt_synct,$opt_syncd, $opt_syncc, $opt_syncdw, $opt_loaddump, $opt_allorg,$opt_snapshot, $opt_removepriv,
+ $opt_syncg,$opt_synct,$opt_syncd, $opt_syncc, $opt_syncdw, $opt_synctable, $opt_synctrackfile, $opt_server, $opt_resetorder,
+ $opt_loaddump, $opt_allorg,$opt_snapshot, $opt_removepriv,
$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, $opt_primers,
@@ -151,13 +152,16 @@
if ($opt_loaddump) { &Load_dbdump(\%global_vars); &Load_desc_page(\%global_vars); }
if ($opt_removepriv) { &Remove_private_genome_hits(\%global_vars); }
if ($opt_initdb) { &Initialize_org_db(\%global_vars); }
+ if ($opt_resetorder) { &Reset_org_order(\%global_vars); }
if ($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"); }
if ($opt_syncc) { &Sync_genome_db(\%global_vars, "collab"); }
if ($opt_syncdw) { &Sync_genome_db(\%global_vars, "download"); }
+ if ($opt_synctable ne '' && $opt_server ne '') { &Sync_table(\%global_vars, $opt_synctable, $opt_server); }
+ if ($opt_synctrackfile ne '' && $opt_server ne '') { &Sync_track_file(\%global_vars, $opt_synctrackfile, $opt_server); }
if ($opt_swissprot ne '') { &Load_swissprot_db(\%global_vars, $opt_swissprot); }
if ($opt_pfamdesc) { &Load_pfam_desc(\%global_vars); }
if ($opt_snapshot ne '') { &Get_snapshot(\%global_vars, $opt_auth); }
if ($opt_initblat) { &Load_blat_info(\%global_vars); }
@@ -406,15 +410,18 @@
$opt_precomp = '';
$opt_swissprot = '';
$opt_annotrev = '';
$opt_genetree = '';
+ $opt_server = '';
+ $opt_synctable = '';
+ $opt_synctrackfile = '';
Getopt::Long::GetOptions("getseqs","joinassembly", "initdb","hidedb","droptable=s","initblat","gc","gbhits","removepriv",
"repeats","iselements", "desc","info","generefs",
"pfam","scanpfam",
"genes","genepred","cogs","kegg","gbrnas","trnas","snornas","delete=s", "igenics",
- "syncg","synct","syncd","syncc","syncdw","loaddump", "swissprot=s", "pfamdesc",
- "rfam","tigr","jgi","easy","startblat","killblat","blatscript","selfz","multiz", "ultracons",
+ "syncg","synct","syncd","syncc","syncdw","synctable=s", "synctrackfile=s", "server=s", "loaddump", "resetorder",
+ "rfam","tigr","jgi","easy","startblat","killblat","blatscript","selfz","multiz", "ultracons", "swissprot=s", "pfamdesc",
"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",
@@ -438,16 +445,20 @@
" --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",
+ " --resetorder: Reset organism display order\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",
- " --syncg : Synchronize /gbdb and mySql db for organism to public server\n",
- " --synct : Synchronize /gbdb and mySql db for organism to testing server\n",
- " --syncd : Synchronize /gbdb and mySql db for organism to development server\n",
- " --syncc : Synchronize /gbdb and mySql db for organism to collaborative server\n",
- " --syncdw : Synchronize /gbdb and mySql db for organism to download server\n",
+ " --syncg : Synchronize /gbdb and MySQL db for organism to public server\n",
+ " --synct : Synchronize /gbdb and MySQL db for organism to testing server\n",
+ " --syncd : Synchronize /gbdb and MySQL db for organism to development server\n",
+ " --syncc : Synchronize /gbdb and MySQL db for organism to collaborative server\n",
+ " --syncdw : Synchronize /gbdb and MySQL db for organism to download server\n",
+ " --synctable=<table> : Synchronize MySQL table for organism to server specified with --server\n",
+ " --synctrackfile=<track> : Synchronize /gbdb track files for organism to server specified with --server\n",
+ " --server=<server> : Use in combination with --synctable or --synctable. Values can public, dev, test, or collab.\n",
" --swissprot=<MMDDYYYY> : Load swissprot data with release date of <MMDDYYYY>\n",
" --pfamdesc : Load Pfam description table into proteome database\n",
" --initblat : Initialize db for Blat Servers\n",
" --startblat : Start blat server (will not start if already running)\n",
@@ -556,8 +567,21 @@
die "Must use --public when running on public or test server\n\n";
}
}
+ if (($opt_synctable ne '' || $opt_synctrackfile ne '') && $opt_server eq '')
+ {
+ die "Must specify destination server using --server when running with option --synctable or --synctrackfile\n";
+ }
+
+ if ($opt_server ne '')
+ {
+ if ($opt_server ne "public" && $opt_server ne "test" && $opt_server ne "dev" && $opt_server ne "collab")
+ {
+ die "Invalid values for --server. Must be public, test, dev, or collab\n";
+ }
+ }
+
if ($global_constants->on_collab() && $opt_altdb ne "" && $opt_multiz)
{
$opt_pubmultiz = 1;
$opt_multiz = 0;