<pre style='margin:0'>
Marcus Calhoun-Lopez (MarcusCalhoun-Lopez) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/f9294a808aeb8e2a95e25d9039fd96aafb3fd33d">https://github.com/macports/macports-ports/commit/f9294a808aeb8e2a95e25d9039fd96aafb3fd33d</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit f9294a808aeb8e2a95e25d9039fd96aafb3fd33d
</span>Author: Marcus Calhoun-Lopez <mcalhoun@macports.org>
AuthorDate: Fri Feb 28 03:39:09 2020 -0700
<span style='display:block; white-space:pre;color:#404040;'> bowtie2: reformat Portfile
</span>---
science/bowtie2/Portfile | 103 ++++++++++++++++++++++++-----------------------
1 file changed, 53 insertions(+), 50 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bowtie2/Portfile b/science/bowtie2/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index f9a7004..e36e912 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bowtie2/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bowtie2/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,75 +1,78 @@
</span> # -*- 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
<span style='display:block; white-space:pre;background:#ffe0e0;'>-PortSystem 1.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-PortGroup github 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortSystem 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup github 1.0
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup BenLangmead bowtie2 2.3.5.1 v
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup BenLangmead bowtie2 2.3.5.1 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-categories science biology
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-platforms darwin
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-license GPL-3+
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-maintainers {mcalhoun @MarcusCalhoun-Lopez} openmaintainer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories science biology
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+platforms darwin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license GPL-3+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers {mcalhoun @MarcusCalhoun-Lopez} openmaintainer
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-description Bowtie 2: Fast and sensitive read alignment
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-long_description Bowtie 2 is an ultrafast and memory-efficient tool \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for aligning sequencing reads to long reference \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sequences. It is particularly good at aligning reads \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- of about 50 up to 100s or 1,000s of characters, and \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- particularly good at aligning to relatively long \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- (e.g. mammalian) genomes. Bowtie 2 indexes the genome \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- with an FM Index to keep its memory footprint small: \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for the human genome, its memory footprint is \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- typically around 3.2 GB. Bowtie 2 supports gapped, \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- local, and paired-end alignment modes.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description Bowtie 2: Fast and sensitive read alignment
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description Bowtie 2 is an ultrafast and memory-efficient tool \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ for aligning sequencing reads to long reference \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sequences. It is particularly good at aligning reads \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ of about 50 up to 100s or 1,000s of characters, and \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ particularly good at aligning to relatively long \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ (e.g. mammalian) genomes. Bowtie 2 indexes the genome \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ with an FM Index to keep its memory footprint small: \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ for the human genome, its memory footprint is \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ typically around 3.2 GB. Bowtie 2 supports gapped, \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ local, and paired-end alignment modes.
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 32fd950a84a901edc8db34a9939c2a7e8c82b8ef \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 663c8d44bea5532a8096d66414885e98f8077177959518015948db034fbdb280 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 10587306
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 32fd950a84a901edc8db34a9939c2a7e8c82b8ef \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 663c8d44bea5532a8096d66414885e98f8077177959518015948db034fbdb280 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 10587306
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles patch-src-Makefile.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles patch-src-Makefile.diff
</span>
post-patch {
<span style='display:block; white-space:pre;background:#ffe0e0;'>- reinplace -W ${worksrcpath} \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- "s|^#!/usr/bin/env python|#!${prefix}/bin/python2.7|" \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2-build \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie2-inspect
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reinplace -W ${worksrcpath} \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ "s|^#!/usr/bin/env python|#!${prefix}/bin/python2.7|" \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bowtie2-build \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bowtie2-inspect
</span> }
<span style='display:block; white-space:pre;background:#ffe0e0;'>-supported_archs x86_64
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-universal_variant no
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-installs_libs no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+supported_archs x86_64
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+universal_variant no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+installs_libs no
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_lib-append port:zlib \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- port:tbb
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append port:zlib \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:tbb
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_run-append port:python27
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_run-append port:python27
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.cmd printenv
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.cmd printenv
</span> configure.pre_args
configure.universal_args
<span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.post_args {>> Makefile.macports.inc}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.post_args {>> Makefile.macports.inc}
</span>
# replicate values from Makefile prior to patching
<span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.optflags -O3 -funroll-loops -g3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.optflags -O3 -funroll-loops -g3
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-destroot.args-append prefix=${prefix}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+destroot.args-append prefix=${prefix}
</span>
post-destroot {
<span style='display:block; white-space:pre;background:#ffe0e0;'>- xinstall -m 755 -d ${destroot}${prefix}/share/doc/${name}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- xinstall -m 644 -W ${worksrcpath} \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- VERSION \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- TUTORIAL \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- README.md \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- NEWS \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- MANUAL.markdown \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- MANUAL \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- LICENSE \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- AUTHORS \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ${destroot}${prefix}/share/doc/${name}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ xinstall -m 755 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -d \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ${destroot}${prefix}/share/doc/${name}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ xinstall -m 644 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -W ${worksrcpath} \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ VERSION \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ TUTORIAL \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ README.md \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ NEWS \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ MANUAL.markdown \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ MANUAL \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ LICENSE \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ AUTHORS \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ${destroot}${prefix}/share/doc/${name}
</span> }
# do not find _new or -beta software
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.livecheck.regex {([^"_-]+)}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.livecheck.regex {([^"_-]+)}
</span></pre><pre style='margin:0'>
</pre>