Commit f9ef540d authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Set new paths, compatible with module

parent bf3e5e97
...@@ -21,7 +21,7 @@ use LWP::Simple; # To test gigablaster availability ...@@ -21,7 +21,7 @@ use LWP::Simple; # To test gigablaster availability
use Mail::Send; # Send warnings and errors files by e-mail ==> only if the $userEMail variable is defined use Mail::Send; # Send warnings and errors files by e-mail ==> only if the $userEMail variable is defined
use lib '/mnt/common/share/ProtoGene/'; # Local path for ProtoGene's own perl modules use lib '/mnt/common/share/ProtoGene/'; # Local path for ProtoGene's own perl modules
use lib '/mnt/local/lib/tcoffee_perl/'; #use lib '/mnt/local/lib/tcoffee_perl/';
use Exonerate; # Exonerate runner, parser, ... use Exonerate; # Exonerate runner, parser, ...
use Views; # Non-text outputs, e.g. HTML/CSS use Views; # Non-text outputs, e.g. HTML/CSS
#use CheckOutput; # Check output for cds consistancy with query #use CheckOutput; # Check output for cds consistancy with query
...@@ -29,9 +29,9 @@ use Views; # Non-text outputs, e.g. HTML/CSS ...@@ -29,9 +29,9 @@ use Views; # Non-text outputs, e.g. HTML/CSS
################## CONFIGURATION ################## ################## CONFIGURATION ##################
$ENV{'PATH'} .= ':/mnt/local/bin/:./'; # Additional path for executables #$ENV{'PATH'} .= ':/mnt/local/bin/:./'; # Additional path for executables
my $cachePath = '/scratch/cluster/monthly/t_coffee/ProtoGene_Cache'; # Cache directory my $cachePath = '/scratch/fhgfs/tcoffee/ProtoGene_Cache'; # Cache directory
my $cacheStorageTime = 15; # Do not update sequences younger than X days my $cacheStorageTime = 15; # Do not update sequences younger than X days
my $userEMail = 'moretti.sebastien@gmail.com'; # To receive e-mails with encountered problems; leave blank to inactive my $userEMail = 'moretti.sebastien@gmail.com'; # To receive e-mails with encountered problems; leave blank to inactive
...@@ -58,8 +58,8 @@ my $blast_param = { 'evalue' => 0.05, ...@@ -58,8 +58,8 @@ my $blast_param = { 'evalue' => 0.05,
my $VERSION = '4.1.0'; my $VERSION = '4.1.0';
my $webblast_exe = '/mnt/common/share/ProtoGene/webblast.pl'; my $webblast_exe = '/mnt/common/share/ProtoGene/webblast.pl';
my $blast_exe = 'blastall'; # Or wu-blastall for Wu-BLAST; for local blast usage my $blast_exe = 'blastall'; # Or wu-blastall for Wu-BLAST; for local blast usage
my $exonerate_exe = 'exonerate-1.0'; # Exonerate 1.0 because current parser only works with this version my $exonerate_exe = 'exonerate'; # Exonerate 1.0 because current parser only works with this version
################## Option management ################## Option management
......
- sort boj pos output - sort boj pos output
- Exonerate 2+ ...
- ssearch instead of blast to be more sensitive ? - ssearch instead of blast to be more sensitive ?
- add "respect case for seq name between in0 and in1" - add "respect case for seq name between in0 and in1"
- add URL to help converting MSA/seq to fasta - add URL to help converting MSA/seq to fasta
......
...@@ -20,13 +20,13 @@ my $ret = GetOptions( 'p=s' => \$program, ...@@ -20,13 +20,13 @@ my $ret = GetOptions( 'p=s' => \$program,
'T=s' => \$html,); 'T=s' => \$html,);
if( $program eq '' ){ if( $program eq '' ){
&Usage(); Usage();
exit(0); exit(0);
} }
my $dbtype = 'NucleotideDatabases'; my $dbtype = 'NucleotideDatabases';
$dbtype = 'ProteinDatabases' if( $program eq 'blastp' || $program eq 'blastx' ); $dbtype = 'ProteinDatabases' if( $program eq 'blastp' || $program eq 'blastx' );
if( $filter eq 'T' || $filter eq 'on' ){ if( $filter eq 'T' || $filter eq 'on' ){
...@@ -36,7 +36,7 @@ else { ...@@ -36,7 +36,7 @@ else {
$filter = 'off'; $filter = 'off';
} }
$html = 'on' if( $html eq 'T' ); $html = 'on' if( $html eq 'T' );
...@@ -60,20 +60,20 @@ my $sequence = ''; ...@@ -60,20 +60,20 @@ my $sequence = '';
if ( $inputfile eq '' ){ if ( $inputfile eq '' ){
while( <STDIN> ){ while( <STDIN> ){
if( /^>/ ){ if( /^>/ ){
&RunBlast() if( $sequence ne '' ); RunBlast() if( $sequence ne '' );
$sequence = $_; $sequence = $_;
} }
else { else {
$sequence .= $_; $sequence .= $_;
} }
} }
&RunBlast(); RunBlast();
} }
elsif ( $inputfile ne ''){ elsif ( $inputfile ne ''){
open(INFILE,"$inputfile") if ( -e "$inputfile" ); open(INFILE,"$inputfile") if ( -e "$inputfile" );
while(<INFILE>){ while(<INFILE>){
if( /^>/ ){ if( /^>/ ){
&RunBlast() if( $sequence ne '' ); RunBlast() if( $sequence ne '' );
$sequence = $_; $sequence = $_;
} }
else { else {
...@@ -82,10 +82,10 @@ elsif ( $inputfile ne ''){ ...@@ -82,10 +82,10 @@ elsif ( $inputfile ne ''){
} }
} }
close INFILE; close INFILE;
&RunBlast(); RunBlast();
} }
else{ else{
&Usage(); Usage();
exit(0); exit(0);
} }
......
...@@ -16,9 +16,7 @@ use warnings; ...@@ -16,9 +16,7 @@ use warnings;
############################ EXPRESSO PARAM ################################################# ############################ EXPRESSO PARAM #################################################
my $database_expresso = 'pdb'; #PDB database name # my $database_expresso = 'pdb'; #PDB database name #
my $blast_dir_expresso = '/mnt/local/bin/blastall'; #blastall executable # my $blast_dir_expresso = 'blastall'; #blastall executable #
my $BLASTMAT = 'export BLASTMAT=/mnt/local/ncbi/data/'; #matrix directory for blast #
my $BLASTDB = 'export BLASTDB=/db/blastnet/database/'; #PDB_seqres directoty #
############################################################################################### ###############################################################################################
my $runblast = 'runblast.pl'; my $runblast = 'runblast.pl';
......
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