bug 2074

svn path=/bioperl-ext/trunk/; revision=678

Bio/SeqIO/staden/CHANGES

@@ -0,0 +1 @@
+071022 - changed from Inline::C to standard xs module

Bio/SeqIO/staden/MANIFEST

@@ -0,0 +1,15 @@
+CHANGES
+Makefile.PL
+MANIFEST			This list of files
+META.yml			Module meta-data (added by MakeMaker)
+read.pm
+read.xs
+README
+t/staden/data/readtest.abi
+t/staden/data/readtest.ctf
+t/staden/data/readtest.exp
+t/staden/data/readtest.pln
+t/staden/data/readtest.ztr
+t/staden/data/readtestabi.fa
+t/staden/data/readtestref.scf
+t/staden_read.t

Bio/SeqIO/staden/META.yml

@@ -0,0 +1,11 @@
+--- #YAML:1.0
+name:                Bio-SeqIO-staden-read
+version:             1.51
+abstract:            ~
+license:             ~
+generated_by:        ExtUtils::MakeMaker version 6.36
+distribution_type:   module
+requires:     
+meta-spec:
+    url:     http://module-build.sourceforge.net/META-spec-v1.2.html
+    version: 1.2

Bio/SeqIO/staden/Makefile.PL

@@ -1,76 +1,129 @@
-use Inline::MakeMaker;
+use ExtUtils::MakeMaker;
 use Config;
+use Cwd qw(realpath);
+use strict;
 
-WriteInlineMakefile(
-		    'NAME'		=> 'Bio::SeqIO::staden::read',
-		    'VERSION_FROM'	=> './read.pm', # finds $VERSION,
-		    'PREREQ_PM'		=> { 'Inline::C' => 0.0,
-					     'Bio::SeqIO::abi' => 0.0,
-					   }, # e.g., Module::Name => 1.1,
-		    test                => { TESTS => 'test.pl' },
-		   );
-
-sub MY::test_via_script {
-    package MY;
-    my $self = shift;
-    return ''; # prevent double-run of test.pl
-}
+my $default_staden_location = '/usr/local/staden/io_lib';
 
-sub MY::post_initialize {
-    package MY;
-    my $self = shift;
+my %options = %{       
+    {
+        'NAME'     => 'Bio::SeqIO::staden::read',
+        'VERSION'  => '1.51'
+    }
+};
 
-    my ($iolibinc, $ioliblib) = @ENV{qw(IOLIB_INC IOLIB_LIB)};
+my ($staden_libs_opts, $staden_include_opts );
 
-    unless ($ioliblib) {
-	($ioliblib) = grep { defined } map { m/^IOLIB_LIB\=(\S+)/o ? $1 : undef } @ARGV;
-    }
-    unless ($iolibinc) {
-	($iolibinc) = grep { defined } map { m/^IOLIB_INC\=(\S+)/o ? $1 : undef } @ARGV;
-    }
+#
+# see if io_lib-config from staden is on the path.
+#  
+# 
+print "Let's see if io_lib-config is on your path\n";
+system("io_lib-config --version");
 
-    # guess wildly!!
-    unless ($ioliblib) {
-	my @d;
-	for my $test (split(/\s+/, $main::Config{libpth}), $self->{LIB}) {
-	    next unless $test;
-	    eval { local $SIG{__WARN__} = sub { }; @d = $self->ext("-L$test -lread") };
-	    if ($d[3] eq $test) {
-		$ioliblib = $test;
-		warn "Found Staden io_lib \"libread\" in $ioliblib ...\n";
-		unless ($iolibinc) {
-		    $iolibinc = $test;
-		    $iolibinc =~ s/lib$/include/;
-		    $iolibinc = $self->catdir($iolibinc, "io_lib");
-		    unless (-e $self->catfile($iolibinc, "Read.h")) {
-			undef $iolibinc;
-		    } else {
-			warn "Automatically using the Read.h found in $iolibinc ...\n";
-		    }
-		}
-		last;
-	    }
-	}
-    }
+if ( $? ) {   # no io_lib-config on path
+  print "Nope, couldn't find io_lib-config on the path\n";
+
+  # try the environment 
 
-    unless ($ioliblib) {
-	$ioliblib = ExtUtils::MakeMaker::prompt("Please tell us where your Staden io_lib \"read\" library is installed: ", "/usr/local/lib");
+  my ($iolibinc, $ioliblib) = @ENV{qw(IOLIB_INC IOLIB_LIB)};
+
+  # try the command line 
+  unless ($ioliblib) {
+    ($ioliblib) = grep { defined } map { m/^IOLIB_LIB\=(\S+)/o ? $1 : undef } @ARGV;
+  }
+  unless ($iolibinc) {
+    ($iolibinc) = grep { defined } map { m/^IOLIB_INC\=(\S+)/o ? $1 : undef } @ARGV;
+  }
+
+  # guess wildly!
+  unless( $ioliblib ) {
+    my @d;
+    for my $test (split(/\s+/, $main::Config{libpth} ) ) { 
+        next unless $test;
+        eval { local $SIG{__WARN__} = sub { }; @d = ExtUtils::Liblist->ext("-L$test -lread") };
+        my ($dir) = split /\s+/, $d[2];
+        if ($dir eq "-L$test") {
+            $ioliblib = $test;
+            warn "Found Staden io_lib \"libread\" in $ioliblib ...\n";
+            unless ($iolibinc) {
+                $iolibinc = $test;
+                $iolibinc =~ s/lib$/include/;
+                my $iolibinc_io_lib = File::Spec->catdir($iolibinc, 'io_lib');
+                unless (-e File::Spec->catfile($iolibinc_io_lib, 'Read.h')) { 
+                    undef $iolibinc;
+                } else {
+                    warn "Found the Read.h found in $iolibinc but lets see what io_lib-config might think...\n";
+                }
+            }
+            last;
+        }
     }
+  }
+
+  # try asking for help.
+
+  my $stadenloc;
+
+  unless ( $ioliblib ) {
+      $stadenloc = ExtUtils::MakeMaker::prompt("Please tell us where your Staden io_lib resides: ", $default_staden_location );
+      $stadenloc = realpath( $stadenloc );
+  }
+ #
+ # use the default if nothing was entered
+ #
 
-    unless ($iolibinc) {
-	my $prompt;
-	if ($ioliblib) {
-	    $prompt = $ioliblib;
-	    $prompt =~ s/lib$/include/;
-	    $prompt = $self->catdir($prompt, "io_lib");
-	} else {
-	    $prompt = "/usr/local/include/io_lib";
-	}
-	$iolibinc = ExtUtils::MakeMaker::prompt("Please tell us where your Staden io_lib \"Read.h\" header is installed: ", $prompt);
+  $stadenloc = $stadenloc ? $stadenloc 
+             : $ioliblib  ? realpath( File::Spec->catdir($ioliblib, '..' ) )
+             : $default_staden_location;
+
+  if ( ! -d $stadenloc ) {
+      warn "WARNING: directory $stadenloc not found";
+  }
+
+  if ( -x File::Spec->catfile( $stadenloc, 'bin', 'io_lib-config' ) ) {
+     ($staden_libs_opts, $staden_include_opts ) 
+              = get_from_ioconfig( File::Spec->catfile( $stadenloc, 'bin', 'io_lib-config') );
+  }
+  else{ 
+      # 
+      # no io_lib-config, try some defaults.
+      #
+
+    $ioliblib ||= File::Spec->catdir( $stadenloc,'lib' ); 
+    unless ( $iolibinc ) {
+      $iolibinc = $ioliblib;
+      $iolibinc =~ s/lib$/include/;
     }
 
-    `perl -pi -e 's{(LIBS\\s*=>\\s*")([^"]+)}{\$1-L$ioliblib -lread -lz};' read.pm`;
-    `perl -pi -e 's{(INC\\s*=>\\s*")([^"]+)}{\$1-I$iolibinc};' read.pm`;
+    $staden_libs_opts = "-L$ioliblib -lz -lm -lread";
+    $staden_include_opts = "-I$iolibinc";
+  }
+}
+else { 
+  print "Yes, found io_lib-config, using it to set flags for read.c\n";
+   ($staden_libs_opts, $staden_include_opts ) 
+          = get_from_ioconfig('io_lib-config');
+}
+
+$options{INC} = $staden_include_opts;
+$options{LIBS} = $staden_libs_opts;
+
+WriteMakefile(%options);
 
-    return '';
+# -- done --
+
+sub get_from_ioconfig {
+    my ( $binary ) = @_;
+
+    my $libs = `$binary --libs`;
+    my $incs = `$binary --cflags`;
+
+    chomp $libs;
+    chomp $incs;
+
+    return( $libs, $incs );
 }
+
+# Remove the Makefile dependency. Causes problems on a few systems.
+# sub MY::makefile { '' }

Bio/SeqIO/staden/README

@@ -0,0 +1,54 @@
+o Version
+
+This version number is from Bioperl-ext version 1.5.1 from CVS HEAD.
+
+o Summary
+
+   Bio::SeqIO::staden::read (Aaron Mackey <amackey@virginia.edu>)
+
+o Installing
+
+ To install
+
+   perl Makefile.PL
+   make
+   make test
+   make install (may need root permissions)
+
+ This extension needs the rest of the main bioperl distribution to
+ function properly.  It is only useful as a helper module for the SeqIO
+ system to read sequence trace files handled by the Staden package's
+ io_lib "read" library.  You should have this library installed prior
+ to installing Bio::SeqIO::staden::read, it's currently available at:
+
+ https://sourceforge.net/project/showfiles.php?group_id=100316
+
+ Currently, the Bio::SeqIO::staden::read extension only works with io_lib
+ v. 1.8.11 or 1.8.12; v. 1.9 and higher have several prototype changes in the
+ "read" library which have broken compatibility in those versions for now.
+ It is possible these changes may be addressed in the future.
+
+ Many users have noted that the io_lib install process often forgets
+ to install the "os.h" file along with the rest of the include files;
+ you may have to do this manually.  If so, you may also have to
+ install the "config.h" file for "os.h" to find all the information it
+ needs.  Finally, you may also need to edit "os.h" to #include
+ <config.h> instead of #include "config.h" if you continue to get
+ undefined symbol errors during compilation.  On some OSes you may in fact
+ have to do the OPPOSITE, meaning change <config.h> to "config.h".
+
+ The bioperl-ext make process will prompt you for the LIB and INCLUDE
+ locations (usually /usr/local/lib and usr/local/include/io_lib,
+ respectively) of the io_lib "libread" library and Read.h header files,
+ after trying to automatically find them.  You may also specify these
+ via the environment variables "IOLIB_LIB" and "IOLIB_INC", or via
+ identically named options to perl Makefile.PL:
+
+   perl Makefile.PL IOLIB_LIB=/opt/lib IOLIB_INC=/opt/include/io_lib
+
+ Ignore any warnings about these options being unknown to MakeMaker.
+
+ A failed compilation is most likely due to an incomplete io_lib
+ installation; make sure that all the required io_lib ".h" files are in
+ place (see above regarding "os.h" and "config.h").
+