mirror of
https://github.com/macports/macports-ports.git
synced 2026-07-12 18:20:25 -07:00
86 lines
2.9 KiB
Tcl
86 lines
2.9 KiB
Tcl
# -*- 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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PortGroup github 1.0
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PortGroup boost 1.0
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github.setup infphilo tophat 2.1.2 v
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# Change github.tarball_from to 'releases' or 'archive' next update
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github.tarball_from tarball
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revision 3
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categories science biology
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license Boost-1
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maintainers {mcalhoun @MarcusCalhoun-Lopez} openmaintainer
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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 \
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mammalian-sized genomes using the ultra high-throughput \
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short read aligner Bowtie, and then analyzes the mapping \
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results to identify splice junctions between exons.
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homepage https://ccb.jhu.edu/software/tophat/
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checksums rmd160 5a5525f810a38efd5d95303224477d62eb2bd110 \
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sha256 ec4c522a1caa6cc7c52e2ed7d60f8cdfb21d010523de93d60c64cd5c1b0f352a \
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size 4538707
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use_autoconf yes
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autoconf.cmd ./bootstrap
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autoconf.args
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patchfiles patch-cflags.diff \
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patch-macports_libs.diff \
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patch-cxx14.diff
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post-patch {
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reinplace -W ${worksrcpath}/src \
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"s|^#!/usr/bin/env python|#!${prefix}/bin/python2.7|" \
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bed_to_juncs \
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contig_to_chr_coords \
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generate_chromosome.py \
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sra_to_solid \
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tophat-fusion-post \
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tophat.py
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}
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# replicate default optimization level
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configure.optflags -O3
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configure.cppflags-prepend -I${prefix}/include/seqan-1 \
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-I${prefix}/include/bam-0.1
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# find correct Boost library
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# allow MacPort to set optimization level
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# avoid conflict with boehmgc
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configure.args-append --with-boost-thread=-mt \
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--enable-optim=no \
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--libdir=${prefix}/libexec/${name}/lib
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# need for autoconf
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depends_build-append port:autoconf \
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port:automake \
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port:libtool
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depends_lib-append port:python27 \
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port:zlib \
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port:samtools-0.1 \
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port:seqan-1
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# TopHat attempts to install its own versions
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depends_run-append port:py27-intervaltree2 \
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port:py27-sortedcontainers
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post-destroot {
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delete \
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${destroot}${prefix}/bin/intervaltree \
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${destroot}${prefix}/bin/sortedcontainers
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}
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# TopHat uses BowTie 2 by default, so make it a runtime dependency
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depends_run-append port:bowtie2
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notes {
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By default, TopHat uses BowTie version 2, so the port bowtie2 was installed as a dependency.
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To use BowTie version 1 as well, please install the port bowtie manually.
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}
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