src/hg/archaeStuff/scripts/make-browser-2.0 1.35
1.35 2009/03/08 21:22:11 pchan
change aero to archdev, lowedev to collab, and isla to test; add functions to load swissprot db and pfam desc
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 1.34
retrieving revision 1.35
diff -b -B -U 4 -r1.34 -r1.35
--- src/hg/archaeStuff/scripts/make-browser-2.0 2 Nov 2008 10:11:12 -0000 1.34
+++ src/hg/archaeStuff/scripts/make-browser-2.0 8 Mar 2009 21:22:11 -0000 1.35
@@ -16,9 +16,9 @@
use archaeBrowser::Constant;
use archaeBrowser::Organism;
use archaeBrowser::GenomeInfo;
use archaeBrowser::ConservedDomains;
-
+use archaeBrowser::ProteinDb;
use archaeBrowser::OrganismDb;
use archaeBrowser::Track;
use archaeBrowser::CDS;
use archaeBrowser::Blat;
@@ -99,9 +99,10 @@
# Program option variables
our ($opt_getseqs, $opt_initdb, $opt_hidedb, $opt_droptable, $opt_initblat, $opt_gc, $opt_repeats, $opt_iselements,
- $opt_desc, $opt_info,$opt_pfam,$opt_scanpfam,$opt_syncg,$opt_synct,$opt_syncd, $opt_syncc, $opt_loaddump, $opt_allorg,$opt_snapshot,
+ $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,
$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, $opt_primers,
@@ -174,8 +175,10 @@
if ($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_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); }
if ($opt_startblat || $opt_all){ &Do_start_blat(\%global_vars); }
if ($opt_killblat) { &Do_kill_blat(\%global_vars); }
@@ -405,14 +408,15 @@
$opt_droptable = '';
$opt_snapshot = '';
$opt_auth = '';
$opt_precomp = '';
+ $opt_swissprot = '';
Getopt::Long::GetOptions("getseqs","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","loaddump",
+ "syncg","synct","syncd","syncc","loaddump", "swissprot=s", "pfamdesc",
"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",
@@ -442,8 +446,10 @@
" --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",
+ " --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",
" --killblat : Kill blat server for species\n",
" --blatscript: Just print shell script to start servers, don't run anything\n",