casa-mp-base

# -*- 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

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PortSystem          1.0

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name                tophat

version             1.2.0

categories          science biology

license             LGPL-3+

platforms           darwin

maintainers         nomaintainer

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description         a fast splice junction mapper for RNA-Seq reads

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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.

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homepage            http://ccb.jhu.edu/software/tophat/

master_sites        ${homepage}downloads/

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checksums           sha1        0e697b16c64fa12180b93ecf87fdf25f722973a5 \

                    rmd160      da62ddc6b2bf8deeda19a95965b1ff2cfd4b95b2

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use_parallel_build  no

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depends_lib         port:zlib \

                    port:samtools \

                    port:bowtie

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# samtools and bowtie are not universal

universal_variant   no

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patchfiles          src_GList.hh.patch

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# 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

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livecheck.type      regex

livecheck.url       [lindex ${master_sites} 0]

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