Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / Paths.pm

diff --git a/binaries/src/jpred/lib/Paths.pm b/binaries/src/jpred/lib/Paths.pm
new file mode 100644 (file)
index 0000000..9fa5ca3
--- /dev/null
+++ b/binaries/src/jpred/lib/Paths.pm
@@ -0,0 +1,125 @@
+package Paths;
+
+use strict;
+use warnings;
+use base qw(Exporter);
+use Sys::Hostname ();
+
+=head1 NAME
+
+Paths - Sets paths for executable programs
+
+=head1 DESCRIPTION
+
+This module gathers together all of the little pieces of information that would other wise be 
+floating around in all of the other modules that run external programs. Namely, the path to 
+the executable and nessecery environment variables. 
+
+Putting it all here should mean that this is the only file that needs updating when their 
+location changes, or it's redeployed. Plus some degree of automagic can be used to try 
+and detect changes.
+
+=cut
+
+our @EXPORT_OK = qw(
+  $ff_bignet
+  $analyze
+  $batchman
+  $sov
+  $pairwise
+  $oc
+  $jnet
+  $fastacmd
+  $hmmbuild
+  $hmmconvert
+  $psiblastbin
+  check_OS
+  setup_env
+);
+
+my $HOME = $ENV{HOME};
+#
+# main production path
+#my $SOFTDIR = '/homes/www-jpred/live/jpred/bin';
+#my $platform_dir = "x86_64";
+#
+# development path
+#my $SOFTDIR = '/homes/www-jpred/devel/jpred/bin';
+#my $platform_dir = "x86_64";
+#
+# my laptop test path
+my $SOFTDIR       = '/home/asherstnev/Projects/Jpred.project/jpred/branches/portable';
+my $platform_name = "x86_64";
+
+our $pairwise    = "$SOFTDIR/$platform_name/pairwise";
+our $oc          = "$SOFTDIR/$platform_name/oc";
+our $jnet        = "$SOFTDIR/$platform_name/jnet";
+our $fastacmd    = "$SOFTDIR/$platform_name/fastacmd";
+our $hmmbuild    = "$SOFTDIR/$platform_name/hmmbuild";
+our $hmmconvert  = "$SOFTDIR/$platform_name/hmmconvert";
+our $psiblastbin = "$SOFTDIR/$platform_name/blastpgp";
+
+# required for training with SNNS, but unused currently
+our $ff_bignet = "$HOME/projects/Jnet/bin/snns/ff_bignet";    # CC modified for new path (SNNS app)
+our $analyze   = "$HOME/projects/Jnet/bin/snns/analyze";      # CC modified for new path (SNNS app)
+our $batchman  = "$HOME/projects/Jnet/bin/snns/batchman";     # CC modified for new path (SNNS app)
+our $sov       = "$HOME/projects/Jnet/bin/sov";
+
+sub setup_env {
+  my $newsoftdir       = shift;
+  my $newplatform_name = shift;
+
+  if ( defined $newsoftdir ) {
+    if ( -d $newsoftdir ) {
+      $SOFTDIR = $newsoftdir;
+    } else {
+      warn "setup_env: directory with Jpred software $newsoftdir does not exist. The default directory is used...\n";
+    }
+  }
+  if ( defined $newplatform_name ) {
+    $platform_name = $newplatform_name;
+  }
+
+  $oc          = "$SOFTDIR/$platform_name/oc";
+  $jnet        = "$SOFTDIR/$platform_name/jnet";
+  $fastacmd    = "$SOFTDIR/$platform_name/fastacmd";
+  $pairwise    = "$SOFTDIR/$platform_name/pairwise";
+  $hmmbuild    = "$SOFTDIR/$platform_name/hmmbuild";
+  $psiblastbin = "$SOFTDIR/$platform_name/blastpgp";
+  $hmmconvert  = "$SOFTDIR/$platform_name/hmmconvert";
+}
+
+sub check_OS {
+  if ( "linux" eq $^O or "Linux" eq $^O ) {
+    my $status = system "uname -m > .platform";
+    open my $PLH, "<", ".platform" or die "can't check platform information";
+    my $plt = <$PLH>;
+    close $PLH;
+    chop $plt;
+    $platform_name = "i686" if ( $plt =~ /i[3-6]86/ );
+  } elsif ( "MSWin32" eq $^O ) {
+    $platform_name = "win";
+  } else {
+    warn "check_OS: unknown platform, I'll try to use x86_64 binaries....";
+  }
+
+#  print "\n\ncheck_OS: SOFTDIR -> $SOFTDIR\n\n";
+
+  $oc          = "$SOFTDIR/$platform_name/oc";
+  $jnet        = "$SOFTDIR/$platform_name/jnet";
+  $fastacmd    = "$SOFTDIR/$platform_name/fastacmd";
+  $pairwise    = "$SOFTDIR/$platform_name/pairwise";
+  $hmmbuild    = "$SOFTDIR/$platform_name/hmmbuild";
+  $psiblastbin = "$SOFTDIR/$platform_name/blastpgp";
+  $hmmconvert  = "$SOFTDIR/$platform_name/hmmconvert";
+
+  return $platform_name;
+}
+
+=head1 AUTOMATED CHANGES
+
+Currently the paths are altered on the basis of per host rules.
+
+=cut
+
+1;