From bce259146b19102a3d01643cf441a6e8d829ff98 Mon Sep 17 00:00:00 2001
From: Daniel Rios <dr2@sanger.ac.uk>
Date: Wed, 6 Aug 2008 09:33:34 +0000
Subject: [PATCH] added option to specify release number
---
misc-scripts/translation_attribs_wrapper.pl | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/translation_attribs_wrapper.pl b/misc-scripts/translation_attribs_wrapper.pl
index df278373e5..d1893f49ce 100644
--- a/misc-scripts/translation_attribs_wrapper.pl
+++ b/misc-scripts/translation_attribs_wrapper.pl
@@ -17,6 +17,7 @@ Required arguments:
--pass=pass password for database
+ --release=release release number
Optional arguments:
@@ -46,7 +47,7 @@ submit jobs to the farm grouping the core databases in patterns
Calculate translation_attributes for all databases in ens-staging
- $ ./translation_attribs_wrapper.pl --user ensadmin --pass password
+ $ ./translation_attribs_wrapper.pl --user ensadmin --pass password --release 51
=head1 LICENCE
@@ -75,6 +76,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw);
my $binpath = '/software/pubseq/bin/emboss';
my $tmpdir = '/tmp';
my $host = 'ens-staging';
+my $release = undef;
my $user = undef;
my $pass = undef;
my $port = 3306;
@@ -88,6 +90,7 @@ GetOptions('binpath=s' => \$binpath,
'user=s' => \$user,
'pass=s' => \$pass,
'port=s' => \$port,
+ 'release=i' => \$release,
'pepstats_only' => \$pepstats_only,
'met_and_stop_only' => \$met_and_stop_only,
'help' => \$help
@@ -96,6 +99,7 @@ GetOptions('binpath=s' => \$binpath,
pod2usage(1) if($help);
throw("--user argument required") if (!defined($user));
throw("--pass argument required") if (!defined($pass));
+throw("--release argument required") if (!defined($release));
my $queue = 'long';
my $memory = "'select[mem>4000] rusage[mem=4000]' -M4000000";
@@ -119,11 +123,11 @@ if (defined $met_and_stop_only){
$options .= "--met_and_stop_only "
}
my @ranges = ('^[a-c]','^[d-g]','^[h-m]','^[n-r]','^[s-z]');
-my $core_db = '.*core_49_.*';
+my $core_db = ".*core_$release\_.*";
my $call;
foreach my $pattern (@ranges){
$call = "bsub -o /lustre/scratch1/ensembl/dr2/tmp_smallfiles/output_translation_$pattern.txt -q $queue -R$memory ./translation_attribs.pl -user $user -pass $pass $options";
- $call .= " --pattern $pattern$core_db";
+ $call .= " --pattern '" . $pattern . $core_db. "'";
system($call);
#print $call,"\n";
--
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