From 5096aae3b192a6b1f32df66c82f2e1cfa668ded8 Mon Sep 17 00:00:00 2001
From: Uma Maheswari <uma@ebi.ac.uk>
Date: Wed, 30 Nov 2011 16:14:15 +0000
Subject: [PATCH] modified to add generic production database details
---
.../density_feature/repeat_coverage_calc.pl | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/density_feature/repeat_coverage_calc.pl b/misc-scripts/density_feature/repeat_coverage_calc.pl
index 30ae76605f..a62366bdc5 100644
--- a/misc-scripts/density_feature/repeat_coverage_calc.pl
+++ b/misc-scripts/density_feature/repeat_coverage_calc.pl
@@ -24,12 +24,20 @@ use strict;
use Getopt::Long;
my ( $host, $user, $pass, $port, $dbname );
+ # Master database location:
+ my ( $mhost, $mport ) = ( 'mysql-eg-pan-1.ebi.ac.uk', '4276' );
+ my ( $muser, $mpass ) = ( 'ensro', undef );
+ my $mdbname = 'ensembl_production';
+
GetOptions( "host|h=s", \$host,
"user|u=s", \$user,
"pass|p=s", \$pass,
"port=i", \$port,
"dbname|d=s", \$dbname,
+ "mhost=s", \$mhost,
+ "mport=i", \$mport,
+ "muser=s", \$muser,
"help" , \&usage
);
@@ -82,10 +90,6 @@ my $analysis = $aa->fetch_by_logic_name('percentagerepeat');
if ( !defined($analysis) ) {
- # Master database location:
- my ( $mhost, $mport ) = ( 'ens-staging1', '3306' );
- my ( $muser, $mpass ) = ( 'ensro', undef );
- my $mdbname = 'ensembl_production';
my $prod_dsn = sprintf( 'DBI:mysql:host=%s;port=%d;database=%s',
$mhost, $mport, $mdbname );
@@ -355,6 +359,12 @@ Usage:
-p|pass Password for user
+ -mhost ensembl_production database host to connect to
+
+ -mport ensembl_production database port to connect to
+
+ -muser ensembl_production database username
+
-d|dbname Database name
-help This message
--
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