diff variant_effect_predictor/Bio/EnsEMBL/Analysis/Programs.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Analysis/Programs.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,196 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+package Bio::EnsEMBL::Analysis::Programs;
+use strict;
+use vars qw( %Program_Paths );
+use Carp;
+use Cwd;
+use Sys::Hostname;
+use Bio::EnsEMBL::Utils::Exception qw ( throw ) ; 
+
+sub import {
+    my $pkg = shift;
+    foreach (@_) {
+        #print STDERR "importing: $_\n";
+        $Program_Paths{ $_ } = 0;
+    }
+    my( $home, @PATH, @missing );
+    
+    $home = cwd() or die "Can't save cwd";
+    my $H = [ $home, 1 ];
+    
+    @PATH = split /:/, $ENV{'PATH'};
+    foreach (@PATH) {
+        s|/?$|/|; # Append / to each path
+    }
+    
+    # For each program, check there is an executable
+    foreach my $program (keys %Program_Paths) {
+        
+        # Deal with paths
+        if ($program =~ m|/|) {
+            _go_home( $H );
+            my $path = $program;
+            # Deal with tildes
+            $path =~ s{^~([^/]*)}{ $1 ? (getpwnam($1))[7]
+                                      : (getpwuid($>))[7] }e;
+            if (my $real = _is_prog( $H, $path )) {
+                $Program_Paths{ $program } = $real;
+            }            
+        }
+        # Or search through all paths
+        else {
+            foreach my $path (@PATH) {
+                _go_home( $H );
+                if (my $real = _is_prog( $H, $path, $program )) {
+                    $Program_Paths{ $program } = $real;
+                    last;
+                }
+            }
+        }
+    }
+    _go_home( $H ); # Return to home directory
+    
+    # Make a list of all missing programs
+    foreach my $program (keys %Program_Paths) {
+        push( @missing, $program ) unless $Program_Paths{ $program };
+    }
+    
+    # Give informative death message if programs weren't found
+    if (@missing) { 
+        throw("Unable to locate the following programs as '". (getpwuid($<))[0]. "' on host '". hostname(). "' :\t".
+        join ( " --> " , @missing )) ; 
+    }
+}
+
+# Recursive function which follows links, or tests final destination
+sub _is_prog {
+    my( $h, $path, $prog ) = @_;
+
+    # Need to split path if $prog not provided
+    unless ($prog) {
+        ($path, $prog) = $path =~ m|(.*?)([^/]+)$|;
+    }
+    
+    if (-l "$path$prog") {
+        # Follow link
+        _follow( $h, $path ) or return;
+        unless (-x readlink($prog)) {
+          confess "Can't read link '$path$prog' : $!";
+	}
+	my $link = $prog;
+	$path = cwd() or confess "Can't determine cwd";
+        return "$path/$prog";
+    } elsif (-f _ and -x _) {
+        # Return full path
+        _follow( $h, $path ) or return;
+        $path = cwd() or confess "Can't determine cwd";
+        return "$path/$prog";
+    } else {
+        # Not a link or an executable plain file
+        return;
+    }
+}
+
+# To avoid unnecessary chdir'ing
+sub _follow {
+    my( $H, $path ) = @_;
+    
+    # Chdir without arguments goes to home dir.
+    # Can't use defined in test since $path may contain
+    # a real null string.
+    if ( ! $path and $path ne '0' ) {
+        return 1;
+    } elsif (chdir($path)) {
+        $H->[1] = 0;
+        return 1;
+    } else {
+        return;
+    }
+}
+sub _go_home {
+    my( $H ) = @_;
+    
+    # Go home unless we're already there
+    if ($H->[1] == 0) {
+        if (chdir( $H->[0] )) {
+            $H->[1] = 1;
+        } else {
+            confess "Can't go home to [ ", $H->[0], ' ]';
+        }
+    }
+}
+
+1;
+
+__END__
+
+=head1 NAME Programs
+
+=head1 SYSNOPSIS
+
+    use Bio::EnsEMBL::Analysis::Programs qw( efetch getz est2genome 
+                     /usr/local/bin/this_one
+                     ~me/some/path/my_prog
+                     ~/../jane/bin/her_prog );
+
+    # Can also do at run time
+    Bio::EnsEMBL::Analysis::Programs->import( $someProg );
+
+    $path_to_prog = $Bio::EnsEMBL::Analysis::Programs::Program_Paths{ $prog };
+
+=head1 DESCRIPTION
+
+B<Programs> is used to check at compile time for the
+presence of executables which will be called from your
+script.  Arguments passed via the use statement
+can be just the program name, or an absolute or
+relative path to the program.  Tildes are expanded
+correctly (I<not> using "glob").  Failure to find any
+one program is fatal, and a list of all failures is
+printed, along with the host''s name.
+
+If you want to check for a program during run time,
+the import funtion can be called directly, as shown above.
+
+The paths to each program found are stored in the
+B<%Program_Paths> hash, which is keyed on the original
+arguments passed.
+
+=head1 BUGS
+
+If the executable is in the root directory, then it''s found
+path will appear as "//prog" in %Program_Paths, not "/prog".
+
+=head1 AUTHOR
+
+B<James Gilbert> Email [e-mail]
+
+
+
+
+
+
+
+
+
+
+