# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
# $Id$

PortSystem          1.0

name                tophat
version             1.2.0
categories          science biology
license             LGPL-3+
platforms           darwin
maintainers         gmail.com:haroldpimentel openmaintainer

description         a fast splice junction mapper for RNA-Seq reads

long_description    TopHat is ${description}. It aligns RNA-Seq reads to \
                    mammalian-sized genomes using the ultra high-throughput \
                    short read aligner Bowtie, and then analyzes the mapping \
                    results to identify splice junctions between exons.

homepage            http://ccb.jhu.edu/software/tophat/
master_sites        ${homepage}downloads/

checksums           sha1        0e697b16c64fa12180b93ecf87fdf25f722973a5 \
                    rmd160      da62ddc6b2bf8deeda19a95965b1ff2cfd4b95b2

use_parallel_build  no

depends_lib         port:zlib \
                    port:samtools \
                    port:bowtie

# samtools and bowtie are not universal
universal_variant   no

patchfiles          src_GList.hh.patch

# defines _POSIX_SOURCE which by itself means 1003.1-1988, but uses fseeko
# which is from 1003.1-2001, and strsep which is a BSD extension
configure.cppflags-append -D_DARWIN_C_SOURCE

livecheck.type      regex
livecheck.url       [lindex ${master_sites} 0]
livecheck.regex     ${name}-(\[0-9.\]+)${extract.suffix}