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        infphilo tophat 2.1.2 v

revision            1

categories          science biology

license             Boost-1

platforms           darwin

maintainers         {mcalhoun @MarcusCalhoun-Lopez} 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            https://ccb.jhu.edu/software/tophat/

​

checksums           rmd160  5a5525f810a38efd5d95303224477d62eb2bd110 \

                    sha256  ec4c522a1caa6cc7c52e2ed7d60f8cdfb21d010523de93d60c64cd5c1b0f352a \

                    size    4538707

​

use_autoconf        yes

autoconf.cmd        ./bootstrap

autoconf.args

​

patchfiles          patch-cflags.diff \

                    patch-macports_libs.diff \

                    patch-cxx14.diff

​

post-patch {

    reinplace -W ${worksrcpath}/src \

        "s|^#!/usr/bin/env python|#!${prefix}/bin/python2.7|" \

        bed_to_juncs \

        contig_to_chr_coords \

        generate_chromosome.py \

        sra_to_solid \

        tophat-fusion-post \

        tophat.py

}

​

# replicate default optimization level

configure.optflags      -O3

​

configure.cppflags-prepend  -I${prefix}/include/seqan-1 \

                            -I${prefix}/include/bam-0.1

​

# find correct Boost library

# allow MacPort to set optimization level

# avoid conflict with boehmgc

configure.args-append   --with-boost-thread=-mt \

                        --enable-optim=no \

                        --libdir=${prefix}/libexec/${name}/lib

​

# need for autoconf

depends_build-append    port:autoconf \

                        port:automake \

                        port:libtool

​

depends_lib-append      port:python27 \