Release not version.

modules/Bio/EnsEMBL/Pipeline/FASTA/Base.pm

@@ -95,8 +95,8 @@ sub old_path {
   my ($self, $species) = @_;
   my $base = $self->param('ftp_dir');
   my $prod = $self->production_name($species);
-  my $version = $self->param('previous_version');
-  my $dir = File::Spec->catdir($base, "release-$version", 'fasta', $prod, 'dna');
+  my $release = $self->param('previous_release');
+  my $dir = File::Spec->catdir($base, "release-$release", 'fasta', $prod, 'dna');
 }
 
 # Closes file handle, and deletes the file stub if it contains no data

modules/Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm

@@ -34,7 +34,7 @@ Allowed parameters are:
 
 =over 8
 
-=item version - Needed to build the target path
+=item release - Needed to build the target path
 
 =item species - Required to indicate which species we are working with
 
@@ -69,7 +69,7 @@ sub param_defaults {
 
 sub fetch_input {
   my ($self) = @_;
-  foreach my $key (qw/data_type species version base_path/) {
+  foreach my $key (qw/data_type species release base_path/) {
     $self->throw("Cannot find the required parameter $key") unless $self->param($key);
   }
   return;
@@ -135,7 +135,7 @@ sub target_file {
   my @name_bits;
   push @name_bits, $self->web_name();
   push @name_bits, $self->assembly();
-  push @name_bits, $self->param('version');
+  push @name_bits, $self->param('release');
   push @name_bits, $self->param('data_type');
   push @name_bits, 'toplevel';
   push @name_bits, 'fa', 'gz';

modules/Bio/EnsEMBL/Pipeline/FASTA/CopyDNA.pm

@@ -25,19 +25,19 @@ Bio::EnsEMBL::Pipeline::FASTA::CopyDNA
 =head1 DESCRIPTION
 
 Performs a find in the DNA dumps directory, for the given species, in the
-previous version FTP dump directory. Any files matching the normal gzipped
+previous release FTP dump directory. Any files matching the normal gzipped
 fasta extension will be copied over to this release's directory.
 
-Previous version is defined as V<version-1>; override this class if your
-definition of the previous version is different. 
+Previous release is defined as V<release-1>; override this class if your
+definition of the previous release is different. 
 
 Allowed parameters are:
 
 =over 8
 
-=item version - Needed to build the target path
+=item release - Needed to build the target path
 
-=item previous_version - Needed to build the source path
+=item previous_release - Needed to build the source path
 
 =item ftp_dir - Current location of the FTP directory for the previous 
                 release. Should be the root i.e. the level I<release-XX> is in
@@ -63,7 +63,7 @@ use File::Spec;
 
 sub fetch_input {
   my ($self) = @_;
-  my @required = qw/version ftp_dir species/;
+  my @required = qw/release ftp_dir species/;
   foreach my $key (@required) {
     $self->throw("Need to define a $key parameter") unless $self->param($key);
   }
@@ -86,10 +86,10 @@ sub run {
 sub new_filename {
   my ($self, $old_filename) = @_;
   my ($old_volume, $old_dir, $old_file) = File::Spec->splitpath($old_filename);
-  my $old_version = $self->param('previous_version');
-  my $version = $self->param('version');
+  my $old_release = $self->param('previous_release');
+  my $release = $self->param('release');
   my $new_file = $old_file;
-  $new_file =~ s/\.$old_version\./.$version./;
+  $new_file =~ s/\.$old_release\./.$release./;
   my $new_path = $self->new_path();
   return File::Spec->catfile($new_path, $new_file);
 }

modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm

@@ -421,7 +421,7 @@ sub _generate_file_name {
   my @name_bits;
   push @name_bits, $self->web_name();
   push @name_bits, $self->assembly();
-  push @name_bits, $self->param('version');
+  push @name_bits, $self->param('release');
   push @name_bits, lc($data_type);
   push @name_bits, $level if $level;
   push @name_bits, $section if $section;

modules/Bio/EnsEMBL/Pipeline/FASTA/ReuseSpeciesFactory.pm

@@ -32,7 +32,7 @@ Allowed parameters are:
 
 =over 8
 
-=item version - Needed to query production with
+=item release - Needed to query production with
 
 =item ftp_dir - If not specified then we cannot reuse
 
@@ -77,7 +77,7 @@ sub param_defaults {
 sub fetch_input {
   my ($self) = @_;
   $self->SUPER::fetch_input();
-  $self->throw("Need to define a version parameter") unless $self->param('version');
+  $self->throw("Need to define a release parameter") unless $self->param('release');
   
   #Calculate quick lookup
   my %force_species_lookup;
@@ -129,8 +129,8 @@ and production_name = ?
 SQL
   my $production_name  = $dba->get_MetaContainer()->get_production_name();
   $dba->dbc()->disconnect_if_idle();
-  my $version = $self->param('version');
-  my $params = [ $version, 'Y', 'Y', 'Genebuild', 'handed_over', $production_name ];
+  my $release = $self->param('release');
+  my $params = [ $release, 'Y', 'Y', 'Genebuild', 'handed_over', $production_name ];
   my $prod_dba = $self->get_production_DBAdaptor();
   my $result = $prod_dba->dbc()->sql_helper()->execute_single_result(-SQL => $sql, -PARAMS => $params);
   $prod_dba->dbc()->disconnect_if_idle();

modules/Bio/EnsEMBL/Pipeline/FASTA/WuBlastIndexer.pm

@@ -27,7 +27,7 @@ Bio::EnsEMBL::Pipeline::FASTA::WuBlastIndexer
 Creates WUBlast indexes of the given GZipped file. The resulting index
 is created under the parameter location I<base_path> in blast and then in a
 directory defined by the type of dump. The type of dump also changes the file
-name generated. Genomic dumps have their release version replaced with the
+name generated. Genomic dumps have their release number replaced with the
 last repeat masked date. 
 
 Allowed parameters are:

modules/Bio/EnsEMBL/Pipeline/PipeConfig/FASTA_conf.pm

@@ -30,9 +30,9 @@ sub default_options {
         
         force_species => [],
         
-        version => software_version(),
+        release => software_version(),
         
-        previous_version => (software_version() - 1),
+        previous_release => (software_version() - 1),
         
         ### SCP code
         
@@ -45,7 +45,7 @@ sub default_options {
         
         ### Defaults 
         
-        pipeline_name => 'fasta_dump_'.$self->o('version'),
+        pipeline_name => 'fasta_dump_'.$self->o('release'),
         
         wublast_exe => 'xdformat',
         blat_exe => 'faToTwoBit',
@@ -261,8 +261,8 @@ sub pipeline_wide_parameters {
         %{ $self->SUPER::pipeline_wide_parameters() },  # inherit other stuff from the base class
         base_path => $self->o('base_path'), 
         db_types => $self->o('db_types'),
-        version => $self->o('version'),
-        previous_version => $self->o('previous_version'),
+        release => $self->o('release'),
+        previous_release => $self->o('previous_release'),
     };
 }