Commit a977e847 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Add a test to check GigaBlaster availability else use NCBI BLAST

parent bc36b0cb
......@@ -13,6 +13,7 @@ use diagnostics;
use Env qw(HOME); # Use only environmental (shell) HOME variable
use File::Basename;
use File::Copy qw(move); # Avoid external 'mv' command usage
use LWP::Simple; # To test gigablaster availability
use lib '/mnt/common/share/ProtoGene/'; # Local path for ProtoGene's own perl modules
use lib '/mnt/local/lib/tcoffee_perl/';
......@@ -34,7 +35,7 @@ $ENV{'PATH'} .= ':/mnt/local/bin/'; # additional path for executable on the serv
my $Version = '3.0.4';
my $Version = '3.2.0';
my $uct = 15; # UpdateCacheThreshold: number of days before update
my $cachedir = '/scratch/frt/tcoffee/ProtoGene_Cache'; # Cache directory
##### User settings ####################################
......@@ -198,11 +199,20 @@ elsif ( exists( $original_seq[0] ) && $original_seq[0] =~ /[acgtu]/i){
undef $fasta_checker;
#Check GigaBlaster status if used
if ( $giga==1 ){
if ( head('http://www.igs.cnrs-mrs.fr/Giga2/~database/remoteblast.cgi') ){
}
else{
$athome = 0;
}
}
#Start main program with version # of programs and list original queries
print "\n\t Protogene\t$Version\t$date\n\n";
open(my $EXONERATEISHERE,"$exonerate --version |");
my $IsExonerateHere=<$EXONERATEISHERE>;
open(my $EXONERATEISHERE, "$exonerate --version |");
my $IsExonerateHere = <$EXONERATEISHERE>;
close $EXONERATEISHERE;
print "\t $IsExonerateHere\n";
undef $IsExonerateHere;
......@@ -210,7 +220,7 @@ undef $Version;
for(my $m=0; $m<=$#original_names; $m++){
print "\t$original_names[$m]\n";
}
$date.="_$$"; #Add PID
$date .= "_$$"; #Add PID
......@@ -498,9 +508,9 @@ PROTOGENE re-builds the original alignment with nucleotidic information it has g
=over 8
=item version 3.0.4
=item version 3.2.0
=item on Sept 10th, 2007
=item on Oct 5th, 2007
=back
......
#
#Version: 3.0.4
#Version: 3.2.0
#OS: Linux
#Author: Sebastien Moretti
#E-mail: moretti.sebastien@gmail.com
#
History of ProtoGene/PACMAN improvements:
3.2.0
Test if Gigablaster is reachable/available then use it else use NCBI blast
3.0.4
Correct fasta headers in advance mode for CDS & CDSP: elements were
duplicated and a > was persistent.
......
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