From 827fd6c25c0b02c2da0b3b90e54a306b46960fac Mon Sep 17 00:00:00 2001
From: Arnaud Kerhornou <arnaud@ebi.ac.uk>
Date: Thu, 8 Dec 2011 11:45:56 +0000
Subject: [PATCH] Added commandline arguments for connecting ensembl_production
db
---
.../density_feature/variation_density.pl | 19 ++++++++++++++-----
1 file changed, 14 insertions(+), 5 deletions(-)
diff --git a/misc-scripts/density_feature/variation_density.pl b/misc-scripts/density_feature/variation_density.pl
index e937a24106..8c2329aca6 100644
--- a/misc-scripts/density_feature/variation_density.pl
+++ b/misc-scripts/density_feature/variation_density.pl
@@ -13,6 +13,10 @@ my $max_slices = 100;
my $bin_count = 150;
my ($host, $user, $pass, $port, $species);
+# Master database location:
+my ( $mhost, $mport ) = ( 'ens-staging1', '3306' );
+my ( $muser, $mpass ) = ( 'ensro', undef );
+my $mdbname = 'ensembl_production';
my ($block_count, $genome_size, $block_size );
@@ -20,6 +24,9 @@ GetOptions( "host|h=s", \$host,
"user|u=s", \$user,
"pass|p=s", \$pass,
"port=i", \$port,
+ "mhost=s", \$mhost,
+ "mport=i", \$mport,
+ "muser=s", \$muser,
"species|s=s", \$species );
@@ -56,11 +63,6 @@ my $analysis = $analysis_adaptor->fetch_by_logic_name('snpdensity');
if ( !defined($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 );
my $prod_dbh = DBI->connect( $prod_dsn, $muser, $mpass,
@@ -196,6 +198,7 @@ Usage:
$0 -h host [-port port] -u user -p password \\
$indent -s species \\
+ $indent [-mhost ensembl_production host] [-mport ensembl_production host] [-muser ensembl_production host] \\
$indent [-help] \\
-h|host Database host to connect to
@@ -208,6 +211,12 @@ Usage:
-s|species Species name
+ -mhost ensembl_production database host to connect to
+
+ -mport ensembl_production database port to connect to
+
+ -muser ensembl_production database username
+
-help This message
--
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