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

​

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}