1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
|
#!/usr/bin/perl
use strict;
use Module::Build;
use Module::Load::Conditional qw(can_load);
my $HeaderFile = "bam.h";
my $LibFile = "libbam.a";
my $ReadLine;
my ($sam_include,$sam_lib) = find_sam(); # may exit with error here
my $class = Module::Build->subclass(code=><<EOF);
sub process_c_bin_files {
my \$self = shift;
chomp(my \$make = `which make`);
chomp(my \$nmake = `which nmake`);
\$make ||= \$nmake;
system "cd c_bin; \$make INCLUDES=-I$sam_include LIBPATH=-L$sam_lib";
mkdir "blib/bin" unless -e "blib/bin";
my \@exec = grep {-x \$_} <c_bin/*>;
\$self->copy_if_modified(from =>\$_,
to_dir => "./blib/bin/",
flatten=>1,
) foreach \@exec;
}
sub ACTION_clean {
my \$self = shift;
\$self->SUPER::ACTION_clean();
system "cd c_bin; make -s clean";
}
EOF
my $build = $class->new(
module_name => 'Bio::SamTools',
dist_version_from => 'lib/Bio/DB/Sam.pm',
dist_author => 'Lincoln Stein <lincoln.stein@gmail.com>',
dist_abstract => 'Perl interface to SamTools library for DNA sequencing',
license => 'perl',
include_dirs => [$sam_include],
extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'],
extra_compiler_flags=>[
# must match DFLAGS in Samtools Makefile
'-D_IOLIB=2','-D_FILE_OFFSET_BITS=64',
# turn off warnings originating in Perl's Newx* calls
'-Wformat=0',
],
c_source => 'c_bin',
c_bin_files => {'./bin/bam2bedgraph' => 'bin/bam2bedgraph'},
build_requires => {
'ExtUtils::CBuilder' => 0,
},
requires => {
'perl' => '5.008',
'Bio::Root::Version' => '1.006009001',
},
# create_makefile_pl => 'passthrough',
);
$build->add_build_element('c_bin');
$build->create_build_script;
exit 0;
sub find_sam {
my ($sam_include,$sam_lib);
if (my $samtools = _samtools()) {
$sam_include = $samtools
if -e "$samtools/$HeaderFile";
$sam_include = "$samtools/include"
if -e "$samtools/include/$HeaderFile";
$sam_lib = $samtools
if -e "$samtools/$LibFile";
$sam_lib = "$samtools/lib"
if -e "$samtools/lib/$LibFile";
}
my @search_path = qw(/ /usr /usr/share /usr/local);
unless ($sam_include) {
for my $p (@search_path) {
$sam_include ||= "$p/include" if
-e "$p/include/$HeaderFile";
}
}
unless ($sam_lib) {
for my $p (@search_path) {
$sam_lib ||= "$p/lib" if
-e "$p/lib/$LibFile";
}
}
unless ($sam_include && $sam_lib) {
print STDOUT "This module requires samtools 0.1.10 or higher (samtools.sourceforge.net).\n";
my $prompt = "Please enter the location of the bam.h and compiled libbam.a files: ";
my $found;
while (!$found) {
my $path = prompt($prompt);
print STDOUT "\n";
last unless $path;
$sam_include = $path
if -e "$path/$HeaderFile";
$sam_include = "$path/include"
if -e "$path/include/$HeaderFile";
$sam_lib = $path
if -e "$path/$LibFile";
$sam_lib = "$path/lib"
if -e "$path/lib/$LibFile";
$found = $sam_include && $sam_lib;
unless ($found) {
print STDOUT "That didn't seem to be right.\n";
$prompt = "Try again, or hit <enter> to cancel: ";
}
}
}
unless ($sam_include && $sam_lib) {
die <<END;
Can\'t find $LibFile and/or $HeaderFile!
If you haven\'t done so already, please compile samtools 0.1.10 or
higher from http://samtools.sourceforge.net and set the SAMTOOLS
environment variable to point to a samtools distribution directory
containing the compiled $LibFile and $HeaderFile files.
END
}
print STDOUT "Found $sam_include/$HeaderFile and $sam_lib/$LibFile.\n";
return ($sam_include,$sam_lib);
}
sub prompt {
my $msg = shift;
unless (defined $ReadLine) {
eval "require Term::ReadLine";
$ReadLine = Term::ReadLine->can('new') || 0;
$ReadLine &&= Term::ReadLine->new(\*STDOUT);
eval {readline::rl_set('TcshCompleteMode','On')};
}
unless ($ReadLine) {
print STDOUT $msg;
chomp (my $in = <>);
return $in;
}
my $in = $ReadLine->readline($msg);
chomp $in;
$in=~ s/\s+//;
$ReadLine->addhistory($in) if $in =~ /\S/;
return $in;
}
sub _samtools {
$ENV{SAMTOOLS} ||
( can_load(modules => {'Alien::SamTools' => undef, 'File::ShareDir' => undef}) &&
File::ShareDir::dist_dir('Alien-SamTools'));
}
|
