# -*- 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
PortGroup           boost 1.0

github.setup        cole-trapnell-lab cufflinks 2.2.1 v
revision            2
checksums           rmd160  6378571ecb06971d1dff5b6ef81a55b36a8be498\
                    sha256  e8316b66177914f14b3a0c317e436d386a46c4c212ca1b2326f89f8a2e08d5ae \
                    size    766280

categories          science biology
platforms           darwin
maintainers         {ryandesign @ryandesign} openmaintainer
license             Boost-1

description         Cufflinks assembles transcripts, estimates their abundances,\
                    and tests for differential expression and regulation in RNA-Seq samples.

long_description    Cufflinks assembles transcripts, estimates their abundances, \
                    and tests for differential expression and regulation in RNA-Seq \
                    samples. It accepts aligned RNA-Seq reads and assembles the \
                    alignments into a parsimonious set of transcripts. \
                    Cufflinks then estimates the relative abundances of these \
                    transcripts based on how many reads support each one.

homepage            http://${github.author}.github.io/${github.project}/
master_sites        ${homepage}assets/downloads/

depends_build       port:samtools

boost.version       1.71

depends_lib         path:share/pkgconfig/eigen3.pc:eigen3 \
                    port:htslib \
                    port:zlib

patchfiles          boost.patch

configure.args      --with-bam=${prefix} \
                    --with-boost=[boost::install_area] \
                    --with-eigen=${prefix} \
                    --with-zlib=${prefix}

# https://github.com/cole-trapnell-lab/cufflinks/issues/17
# https://github.com/cole-trapnell-lab/cufflinks/issues/100
configure.cppflags-append \
                    -isystem${prefix}/include/eigen3

configure.ldflags-append \
                    -lboost_serialization-mt \
                    -lboost_thread-mt

# https://github.com/cole-trapnell-lab/cufflinks/issues/62
configure.ldflags-append \
                    -lhts

post-destroot {
    set docdir ${prefix}/share/doc/${subport}
    xinstall -d ${destroot}${docdir}
    xinstall -m 0644 -W ${worksrcpath} \
        AUTHORS \
        LICENSE \
        README \
        ${destroot}${docdir}
}