more renaming

[biopieces.git] / code_perl / Maasha / Config.pm

diff --git a/code_perl/Maasha/Config.pm b/code_perl/Maasha/Config.pm
index e25f3f2d7b0286156eea61329261878a98134764..b71397394b55ff8397607fafe450abf6847eb22e 100644 (file)
--- a/code_perl/Maasha/Config.pm
+++ b/code_perl/Maasha/Config.pm
@@ -38,19 +38,19 @@ use vars qw( @ISA @EXPORT );
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GLOBALS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $HOME, $PATH, $DATA_DIR, $TMP_DIR, $INST_DIR );
+my ( $HOME, $PATH, $BP_DATA, $BP_TMP, $BP_DIR );
 
 $HOME     = $ENV{ "HOME" };     
 $PATH     = $ENV{ "PATH" };     
-$DATA_DIR = $ENV{ "DATA_DIR" }; 
-$TMP_DIR  = $ENV{ "TMP_DIR" };  
-$INST_DIR = $ENV{ "INST_DIR" };
+$BP_DIR   = $ENV{ "BP_DIR" };
+$BP_DATA  = $ENV{ "BP_DATA" }; 
+$BP_TMP   = $ENV{ "BP_TMP" };  
 
 warn qq(WARNING: HOME not set in env\n)     if not defined $HOME;
 warn qq(WARNING: PATH not set in env\n)     if not defined $PATH;
-warn qq(WARNING: DATA_DIR not set in env\n) if not defined $DATA_DIR;
-warn qq(WARNING: TMP_DIR not set in env\n)  if not defined $TMP_DIR;
-warn qq(WARNING: INST_DIR not set in env\n) if not defined $INST_DIR;
+warn qq(WARNING: BP_DIR not set in env\n)   if not defined $BP_DIR;
+warn qq(WARNING: BP_DATA not set in env\n)  if not defined $BP_DATA;
+warn qq(WARNING: BP_TMP not set in env\n)   if not defined $BP_TMP;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -90,7 +90,7 @@ sub genome_fasta
 
     # Returns string.
 
-    my $genome_file = "$DATA_DIR/genomes/$genome/$genome.fna";
+    my $genome_file = "$BP_DATA/genomes/$genome/$genome.fna";
 
     if ( not -f $genome_file ) {
         &Maasha::Common::error( qq(Genome file "$genome_file" for genome "$genome" not found) );
@@ -112,7 +112,7 @@ sub genome_fasta_index
 
     # Returns string.
 
-    my $index = "$DATA_DIR/genomes/$genome/$genome.fna.index";
+    my $index = "$BP_DATA/genomes/$genome/$genome.fna.index";
 
     if ( not -f $index ) {
         &Maasha::Common::error( qq(Index file "$index" for genome -> $genome not found) );
@@ -133,7 +133,7 @@ sub genome_blast
 
     # Returns string.
 
-    my $file = "$DATA_DIR/genomes/$genome/blast/$genome.fna";
+    my $file = "$BP_DATA/genomes/$genome/blast/$genome.fna";
 
     return $file;
 }
@@ -152,7 +152,7 @@ sub genome_blat_ooc
 
     # Returns string.
 
-    my $ooc_file = "$DATA_DIR/genomes/$genome/blat/$tile_size.ooc";
+    my $ooc_file = "$BP_DATA/genomes/$genome/blat/$tile_size.ooc";
 
     &Maasha::Common::error( qq(ooc file "$ooc_file" not found for genome -> $genome) ) if not -f $ooc_file;
 
@@ -175,7 +175,7 @@ sub genome_vmatch
 
     @chrs = &chromosomes( $genome );
 
-    map { $_ = "$DATA_DIR/genomes/$genome/vmatch/$_" } @chrs;
+    map { $_ = "$BP_DATA/genomes/$genome/vmatch/$_" } @chrs;
 
     # needs robustness check
 
@@ -195,7 +195,7 @@ sub genome_phastcons
 
     # Returns a string.
     
-    my $file = "$DATA_DIR/genomes/$genome/phastcons/$genome.pp";
+    my $file = "$BP_DATA/genomes/$genome/phastcons/$genome.pp";
 
     return $file;
 }
@@ -213,7 +213,7 @@ sub genome_phastcons_index
 
     # Returns a string.
     
-    my $file = "$DATA_DIR/genomes/$genome/phastcons/$genome.pp.index";
+    my $file = "$BP_DATA/genomes/$genome/phastcons/$genome.pp.index";
 
     return $file;
 }
@@ -230,7 +230,7 @@ sub genomes
 
     my ( %genome_hash, $fh, $line, @genomes, $org );
 
-    $fh = &Maasha::Common::read_open( "$INST_DIR/conf/genomes.conf" );
+    $fh = &Maasha::Common::read_open( "$BP_DIR/conf/genomes.conf" );
 
     while ( $line = <$fh> )
     {
@@ -265,7 +265,7 @@ sub chromosomes
 
     my ( $fh_in, $line, $org, $chr, %genome_hash, @chrs );
 
-    $fh_in = &Maasha::Common::read_open( "$INST_DIR/conf/genomes.conf" );
+    $fh_in = &Maasha::Common::read_open( "$BP_DIR/bp_conf/genomes.conf" );
 
     while ( $line = <$fh_in> )
     {