# -*- 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 bowtie 1.3.1 v revision 0 categories science biology platforms darwin maintainers {mcalhoun @MarcusCalhoun-Lopez} openmaintainer license Artistic-1 LGPL-3+ description an ultrafast, memory-efficient short read aligner long_description Bowtie is ${description}. It aligns short DNA sequences \ (reads) to the human genome at a rate of over 25 million \ 35-bp reads per hour. Bowtie indexes the genome with a \ Burrows-Wheeler index to keep its memory footprint small: \ typically about 2.2 GB for the human genome (2.9 GB for \ paired-end). homepage http://bowtie-bio.sourceforge.net/ checksums rmd160 c4aeaa1135bd40bbcbc38235878644d3b2b219da \ sha256 1e087c6bef7415419902d06b5a4f9d5180fd1daf39b3752044e6b448e46e6a1b \ size 7673131 patchfiles-append patch-Makefile.diff post-patch { reinplace -W ${worksrcpath} \ "s|^#!/usr/bin/env python|#!${prefix}/bin/python2.7|" \ bowtie \ bowtie-build \ bowtie-inspect } # fix build on case insensitive FS # In file included from bowtie_inspect.cpp:1: # In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/c++/v1/string:519: # In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/c++/v1/__debug:21: # In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/c++/v1/cstddef:37: # ./version:1:1: error: expected unqualified-id # 1.3.1 post-extract { file delete ${worksrcpath}/VERSION } compiler.cxx_standard 2011 supported_archs x86_64 ppc64 installs_libs no depends_build-append port:seqan-1 depends_lib-append port:zlib depends_run-append port:python27 # replicate values from Makefile prior to patching configure.optflags -O3 configure.cppflags-prepend \ -I${prefix}/include/seqan-1 configure.cmd printenv configure.pre_args configure.universal_args configure.post_args {>> Makefile.macports.inc} destroot.args-append prefix=${prefix} post-destroot { xinstall -d ${destroot}${prefix}/share/doc/${name} xinstall -m 644 -W ${worksrcpath} \ AUTHORS \ LICENSE \ MANUAL \ NEWS \ TUTORIAL \ MANUAL.markdown \ ${destroot}${prefix}/share/doc/${name} }