# -*- 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
PortGroup           github 1.0

github.setup        BenLangmead bowtie2 2.2.9 v

categories          science biology
platforms           darwin
license             GPL-3
maintainers         mit.edu:gaberoo \
                    openmaintainer

description         Bowtie 2: Fast and sensitive read alignment
long_description    Bowtie 2 is an ultrafast and memory-efficient tool \
                    for aligning sequencing reads to long reference \
                    sequences. It is particularly good at aligning reads \
                    of about 50 up to 100s or 1,000s of characters, and \
                    particularly good at aligning to relatively long \
                    (e.g. mammalian) genomes. Bowtie 2 indexes the genome \
                    with an FM Index to keep its memory footprint small: \
                    for the human genome, its memory footprint is \
                    typically around 3.2 GB. Bowtie 2 supports gapped, \
                    local, and paired-end alignment modes.

homepage            http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

checksums           rmd160  4d385888f4cc1dc465cdd74b2e735ca2baed90e8 \
                    sha256  435c27c33807be6227b5370f53146a3e7f890534db650d3d0f5e86570f9d5170

patchfiles          patch-src-Makefile.diff

use_configure       no
universal_variant   no

build.args-append   CC=${configure.cc} \
                    CXX=${configure.cxx} \
                    CPP=${configure.cpp}

destroot {
    xinstall -m 755 -W ${worksrcpath} \
        bowtie2 \
        bowtie2-align-s \
        bowtie2-align-l \
        bowtie2-build \
        bowtie2-build-s \
        bowtie2-build-l \
        bowtie2-inspect \
        bowtie2-inspect-s \
        bowtie2-inspect-l \
        ${destroot}${prefix}/bin

    xinstall -m 755 -d ${destroot}${prefix}/share/doc/${name}
    xinstall -m 644 -W ${worksrcpath} \
        VERSION \
        TUTORIAL \
        README \
        NEWS \
        MANUAL.markdown \
        MANUAL \
        LICENSE \
        AUTHORS \
        ${destroot}${prefix}/share/doc/${name}
}