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Author: Andreas Tille <tille@debian.org>
Last-Update: 2019-07-10
Description: Take over changes in Build.PL from commit 83c9327 to make sure htslib will be found
--- a/Build.PL
+++ b/Build.PL
@@ -1,6 +1,6 @@
#!/usr/bin/perl
-# Copyright [2015-2018] EMBL-European Bioinformatics Institute
+# Copyright [2015-2019] EMBL-European Bioinformatics Institute
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
@@ -75,7 +75,15 @@ sub find_hts {
# 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')) {
+ my $incdir = $self->args('htslib-includedir');
+ my $libdir = $self->args('htslib-libdir');
+ if ($incdir && $libdir) {
+ return 1 if $self->find_hts_in_split_install_dirs($incdir, $libdir);
+ $self->die_hts_not_found(
+ "--htslib-includedir '$incdir' or --htslib-libdir '$libdir' command line parameters do not contain expected files\n"
+ );
+ }
+ elsif (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(
@@ -105,6 +113,9 @@ sub find_hts {
}
return 1 if $found;
+ # Try pkgconfig again but this time trust whatever it returns, without extra verification
+ return 1 if $self->find_hts_with_pkgconfig();
+
$self->die_hts_not_found();
}
@@ -114,12 +125,14 @@ sub set_include_and_compiler_flags {
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){
- $self->extra_linker_flags("-L$hts_lib", '-lhts', '-lpthread', '-lz');
- }else{
- $self->extra_linker_flags("-L$hts_lib", "-Wl,-rpath,$hts_lib", '-lhts', '-lpthread', '-lz');
+
+ $self->include_dirs([$hts_include]) if $hts_include;
+
+ my @linker_dirflags;
+ if ($hts_lib) {
+ push @linker_dirflags, "-L$hts_lib";
}
+ $self->extra_linker_flags(@linker_dirflags, '-lhts', '-lpthread', '-lz');
}
sub hts_dev_files_exist {
@@ -165,6 +178,48 @@ sub find_hts_in_install_dir {
}
}
+sub find_hts_in_split_install_dirs {
+ my ($self, $hts_include, $hts_lib) = @_;
+
+ chomp($hts_lib);
+ chomp($hts_include);
+ $hts_include =~ s{include/htslib$}{include};
+
+ if (hts_dev_files_exist($hts_lib, $hts_include)) {
+ $self->config_data('hts_lib' => $hts_lib);
+ $self->config_data('hts_include' => $hts_include);
+ return 1;
+ }
+ else {
+ return 0;
+ }
+}
+
+sub find_hts_with_pkgconfig {
+ my ($self) = @_;
+
+ return 0 unless can_load(
+ modules => { 'ExtUtils::PkgConfig' => undef }
+ );
+ my $pkg_name = 'htslib';
+ return 0 unless ExtUtils::PkgConfig->exists($pkg_name);
+
+ if (my $libs_only_L = ExtUtils::PkgConfig->libs_only_L($pkg_name)) {
+ # For compatibility with other htslib search methods. Note that this
+ # assumes there will be at most one each of -I/-L directories, which
+ # is true as of htslib-1.5 but might change in the future.
+ $libs_only_L =~ s{^-L}{};
+ $self->config_data('hts_lib' => $libs_only_L);
+ }
+ if (my $cflags_only_I = ExtUtils::PkgConfig->cflags_only_I($pkg_name)) {
+ # See above
+ $cflags_only_I =~ s{^-I}{};
+ $self->config_data('hts_include' => $cflags_only_I);
+ }
+
+ return 1;
+}
+
sub die_hts_not_found {
my ($self, $msg) = @_;
@@ -177,12 +232,17 @@ Install it if you have not done so alrea
This script will attempt to locate HTSlib by looking for htslib/hts.h
and libhts.a / libhts.so in:
- 1. --htslib command line argument
- 2. HTSLIB_DIR environment variable
- 3. --prefix command line argument (which also sets installation location)
- 4. Alien::HTSlib dependency resolver
- 5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
- 6. common library locations: /usr /usr/local, /usr/share, /opt/local
+ 1. --htslib-includedir and --htslib-libdir command line arguments
+ 2. --htslib command line argument
+ 3. HTSLIB_DIR environment variable
+ 4. --prefix command line argument (which also sets installation location)
+ 5. Alien::HTSlib dependency resolver
+ 6. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
+ 7. common library locations: /usr /usr/local, /usr/share, /opt/local
+
+If none of the above succeeds but htslib is registered with pkg-config, the script
+will try using pkg-config paths (via ExtUtils::PkgConfig) without checking if header
+and library files exist.
END
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