Merge branch 'master' of depot.biologie.ens.fr:rsat

rsa-tools · Jan 19, 2020 · 3ed10ad · 3ed10ad
2 parents f276915 + 60b5f69
commit 3ed10ad
Show file tree

Hide file tree

Showing 3 changed files with 32 additions and 2 deletions.
diff --git a/perl-scripts/download-ensembl-genome b/perl-scripts/download-ensembl-genome
@@ -219,7 +219,7 @@ package	main;
 
   ################################################################
   ## Get Adaptators
-  &RSAT::message::TimeWarn("Getting species adaptor from Ensembl") if ($main::verbose >= 2);
+  &RSAT::message::TimeWarn("Getting species adaptor from Ensembl") if ($main::verbose >= 2);
   my $slice_adaptor = $registry->get_adaptor($species, 'core', 'slice');
   if ($slice_adaptor) {
     &RSAT::message::Debug("Slice adaptor", $slice_adaptor) if ($main::verbose >= 5);

diff --git a/perl-scripts/install-organism b/perl-scripts/install-organism
@@ -987,6 +987,31 @@ sub UpdateConfigTab {
     $supported_organism{$organism_short_name}->{'up_from'} = $args{up_from};
   }
 
+  ## Update blast column in config table if blast information is available
+
+  my $blast_folder=$supported_organism{$organism_short_name}->{'data'}."/blast_hits" ;
+  print "genome folder ". $genome_folder."\n";
+  if ( -d $blast_folder ){
+    $supported_organism{$organism_short_name}->{'blast_available'}= 1;
+  } else {
+    $supported_organism{$organism_short_name}->{'blast_available'}= 0;
+  }
+  ## Update variant columns in config table if variant information
+  my $variants_folder=$supported_organism{$organism_short_name}->{'data'}."/variations" ;
+
+  print "variants folder" . $variants_folder."\n"; 
+  if ( -d $variants_folder ){
+    $supported_organism{$organism_short_name}->{'variant_available'}= 1;
+    my $variant_source = `cat $variants_folder/source.txt`;
+    chomp($variant_source);
+    $supported_organism{$organism_short_name}->{'variant_source'}= $variants_source || "<NA>";
+    $supported_organism{$organism_short_name}->{'path_to_variant_files'}= $variants_folder;
+  } else {
+    $supported_organism{$organism_short_name}->{'variant_available'}= 0; 
+    $supported_organism{$organism_short_name}->{'variant_source'}= "<NA>";
+    $supported_organism{$organism_short_name}->{'path_to_variant_files'}= "<NA>";
+  }
+
 
   &RSAT::message::Debug("&UpdateConfigTab()",
 			$supported_organism{$organism_short_name}->{'source'},
@@ -995,8 +1020,13 @@ sub UpdateConfigTab {
 			$supported_organism{$organism_short_name}->{'last_update'},
 			$supported_organism{$organism_short_name}->{'up_from'},
 			$supported_organism{$organism_short_name}->{'name'},
+			$supported_organism{$organism_short_name}->{'variant_available'},
+			$supported_organism{$organism_short_name}->{'variant_source'},
+			$supported_organism{$organism_short_name}->{'path_to_variant_files'}
       ) if ($main::verbose >= 3);
 
+
+
   ## Export the updated table of supported organisms
   &RSAT::OrganismManager::export_supported_organisms(file=>$main::org_table, backup=>$main::backup_org_table);
 }

diff --git a/public_html/supported-organisms.cgi b/public_html/supported-organisms.cgi
@@ -61,7 +61,7 @@ if ($ENV{group_specificity}) {
 }
 
 ## Export the table with header and absolute paths
-my $organism_table = &RSAT::OrganismManager::supported_organism_table(1, 0, $source, $taxon, $group, $depth, 0, 0, @return_fields); 
+my $organism_table = &RSAT::OrganismManager::supported_organism_table(1, 0, $source, $taxon, $group, $depth, 0, 0, @return_fields);
 my @organism_rows = split("\n", $organism_table);
 my $nb_organisms = scalar(@organism_rows) - 1;