build.cufflinks

#!/usr/bin/env perl

use strict;

use Carp;
use File::Basename;
use Cwd 'abs_path';

my @parallel = ("-j", 8);

my $dest = $ENV{TARGET} || "/kb/runtime";
my $build_tools = $ENV{BUILD_TOOLS} || "/disks/patric-common/runtime/gcc-4.9.3";

if (@ARGV)
{
    $dest = shift;
    print STDERR "Overriding destination to $dest\n";
}

$ENV{PATH} = "$build_tools/bin:$ENV{PATH}";
$ENV{PATH} = "$dest/bin:$ENV{PATH}";
$ENV{CFLAGS} = "-I$dest/include";
$ENV{LDFLAGS} = "-Wl,-rpath,$build_tools/lib64 -Wl,-rpath,$build_tools/lib";

-d $dest || mkdir $dest;


my $hash = "753c109e31818dcf7aa8a2c8ecdac4fa43d2ab9b";

my $cuff_dir = "cufflinks";
system("rm", "-rf", $cuff_dir);
run("git", "clone", 'https://github.com/cole-trapnell-lab/cufflinks.git');

chdir($cuff_dir) || die "cannot chdir $cuff_dir: $!";
run("git", "checkout", $hash);
run("./autogen.sh");
run("./configure", "--with-bam=$dest/samtools", "--prefix=$dest", 
	#"--with-boost-thread=$build_tools/lib/libboost_thread-mt.so", 
	"--with-boost=$build_tools", "--with-boost-libdir=$build_tools/lib");
run("make", @parallel);
run("make", "install");

sub run
{
    my(@cmd) = @_;
    print "@cmd\n";
    my $rc = system(@cmd);
    $rc == 0 or die "Cmd failed with rc=$rc: @cmd\n";
}