Bio-DB-HTS

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Build.PL  view on Meta::CPAN

sub find_hts {
    my ($self) = @_;

    # If either of these are set, we expect to find the htslib files there:
    # (They're explicitly set by the user, so we shouldn't fall back to
    # finding another copy somewhere else.)
    if (my $dir = $self->args('htslib')) {
        return 1 if $self->find_hts_in_build_dir($dir);
        return 1 if $self->find_hts_in_install_dir($dir);
        $self->die_hts_not_found(
            "--htslib '$dir' command line parameter does not contain expected files\n"
        );
    }
    elsif ($dir = $ENV{'HTSLIB_DIR'}) {
        return 1 if $self->find_hts_in_build_dir($dir);
        return 1 if $self->find_hts_in_install_dir($dir);
        $self->die_hts_not_found(
            "HTSLIB_DIR=$ENV{HTSLIB_DIR} environment variable does not contain expected files\n"
        );
    }

    # Search through remaining possible (but not fatal) locations:
    my $found = 0;
    foreach my $dir (
        $self->prefix,
        from_Alien(),
        scalar `pkg-config --variable=libdir htslib 2>/dev/null`,
        qw{ /usr /usr/local /usr/share /opt/local },
    ) {
        if ($dir and $self->find_hts_in_install_dir($dir)) {
            $found = 1;
            last;
        }
    }
    return 1 if $found;

    $self->die_hts_not_found();
}

sub set_include_and_compiler_flags {
    my ($self) = @_;

    my $hts_include = $self->config_data('hts_include');
    my $hts_lib     = $self->config_data('hts_lib');
    my $static      = $self->args('static');
    $self->include_dirs([$hts_include]);
    if($static){

Build.PL  view on Meta::CPAN

    if (hts_dev_files_exist($hts_lib, $hts_include)) {
        $self->config_data('hts_lib'     => $hts_lib);
        $self->config_data('hts_include' => $hts_include);
        return 1;
    }
    else {
        return 0;
    }
}

sub die_hts_not_found {
    my ($self, $msg) = @_;

    $msg ||= '';
    die $msg, <<END;

This module requires HTSlib (http://htslib.org/)
Install it if you have not done so already.

This script will attempt to locate HTSlib by looking for htslib/hts.h
and libhts.a / libhts.so in:

ppport.h  view on Meta::CPAN

new_stackinfo||5.005000|
new_version||5.009000|
new_warnings_bitfield|||
next_symbol|||
nextargv|||
nextchar|||
ninstr|||
no_bareword_allowed|||
no_fh_allowed|||
no_op|||
not_a_number|||
nothreadhook||5.008000|
nuke_stacks|||
num_overflow|||n
offer_nice_chunk|||
oopsAV|||
oopsHV|||
op_clear|||
op_const_sv|||
op_dump||5.006000|
op_free|||

ppport.h  view on Meta::CPAN

#define DPPP_CAT2(x,y) CAT2(x,y)
#define DPPP_(name) DPPP_CAT2(DPPP_NAMESPACE, name)

#ifndef PERL_REVISION
#  if !defined(__PATCHLEVEL_H_INCLUDED__) && !(defined(PATCHLEVEL) && defined(SUBVERSION))
#    define PERL_PATCHLEVEL_H_IMPLICIT
#    include <patchlevel.h>
#  endif
#  if !(defined(PERL_VERSION) || (defined(SUBVERSION) && defined(PATCHLEVEL)))
#    include <could_not_find_Perl_patchlevel.h>
#  endif
#  ifndef PERL_REVISION
#    define PERL_REVISION       (5)
     /* Replace: 1 */
#    define PERL_VERSION        PATCHLEVEL
#    define PERL_SUBVERSION     SUBVERSION
     /* Replace PERL_PATCHLEVEL with PERL_VERSION */
     /* Replace: 0 */
#  endif
#endif