From 7b86113e2cf7ac61ef09cc34c156b3f3da007f28 Mon Sep 17 00:00:00 2001 From: Donnie Berkholz Date: Mon, 11 Dec 2006 06:59:29 +0000 Subject: [PATCH] New package: Protein multiple-alignment-based sequence annealing. It's based on ProbCons and adds sequence annealing. See the homepage for details. Package-Manager: portage-2.1.2_rc3-r1 --- sci-biology/amap/ChangeLog | 11 ++++++ sci-biology/amap/Manifest | 20 +++++++++++ sci-biology/amap/amap-2.0.ebuild | 34 +++++++++++++++++++ sci-biology/amap/files/2.0-fix-cxxflags.patch | 21 ++++++++++++ sci-biology/amap/files/digest-amap-2.0 | 3 ++ sci-biology/amap/metadata.xml | 5 +++ 6 files changed, 94 insertions(+) create mode 100644 sci-biology/amap/ChangeLog create mode 100644 sci-biology/amap/Manifest create mode 100644 sci-biology/amap/amap-2.0.ebuild create mode 100644 sci-biology/amap/files/2.0-fix-cxxflags.patch create mode 100644 sci-biology/amap/files/digest-amap-2.0 create mode 100644 sci-biology/amap/metadata.xml diff --git a/sci-biology/amap/ChangeLog b/sci-biology/amap/ChangeLog new file mode 100644 index 000000000000..d4819372f458 --- /dev/null +++ b/sci-biology/amap/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-biology/amap +# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.1 2006/12/11 06:59:29 dberkholz Exp $ + +*amap-2.0 (11 Dec 2006) + + 11 Dec 2006; Donnie Berkholz ; + +files/2.0-fix-cxxflags.patch, +metadata.xml, +amap-2.0.ebuild: + New package: Protein multiple-alignment-based sequence annealing. It's based + on ProbCons and adds sequence annealing. See the homepage for details. + diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest new file mode 100644 index 000000000000..4613eadbc095 --- /dev/null +++ b/sci-biology/amap/Manifest @@ -0,0 +1,20 @@ +AUX 2.0-fix-cxxflags.patch 835 RMD160 d31c598e91e58ada05320f8c536a2b61c4d50f5d SHA1 42911d9882e4c359f68e318fe65efb9f877fb680 SHA256 fe3e568f785d1d4ee28deeb62cba28aa700066bab7d41828c84d9fcc612fff4e +MD5 76ed725e190bde137cbee78a6d4771ce files/2.0-fix-cxxflags.patch 835 +RMD160 d31c598e91e58ada05320f8c536a2b61c4d50f5d files/2.0-fix-cxxflags.patch 835 +SHA256 fe3e568f785d1d4ee28deeb62cba28aa700066bab7d41828c84d9fcc612fff4e files/2.0-fix-cxxflags.patch 835 +DIST amap.2.0.tar.gz 42389 RMD160 1577da7c930dc72aadda095b24107f933bde4006 SHA1 9a6c083e868ae85ae177445d284dd4c54422e4ef SHA256 3930c4b5d149f01277bc6de2339c5f058d7d2ca36f69f328f1dac2f1a4b5ba92 +EBUILD amap-2.0.ebuild 801 RMD160 21aab7ea289680bd65caa731962ed599716177b9 SHA1 7612a7d574fd59fe18c0dcb54f0ba1322ec561f7 SHA256 b15121d2b7daa8ef42d8bbee88b1c78a085c122a2978deb9ba1408aed35d3036 +MD5 3657e7ca2e283eba851217b4140a8e39 amap-2.0.ebuild 801 +RMD160 21aab7ea289680bd65caa731962ed599716177b9 amap-2.0.ebuild 801 +SHA256 b15121d2b7daa8ef42d8bbee88b1c78a085c122a2978deb9ba1408aed35d3036 amap-2.0.ebuild 801 +MISC ChangeLog 507 RMD160 6e825c7e091cb0a6bb46d8faae6b5a6e326c5f2a SHA1 c314a34e3b92104f34446898495cb21323ecceef SHA256 b112da675d039557f89d77038d2551b5545a7a064c9d2da701f59732ecf01331 +MD5 3fa86e42a4d24ac84a64302e077cede4 ChangeLog 507 +RMD160 6e825c7e091cb0a6bb46d8faae6b5a6e326c5f2a ChangeLog 507 +SHA256 b112da675d039557f89d77038d2551b5545a7a064c9d2da701f59732ecf01331 ChangeLog 507 +MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f +MD5 86813ca8050bc98ba326cb74e88150a5 metadata.xml 164 +RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c metadata.xml 164 +SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f metadata.xml 164 +MD5 5510a75e0abff7dfa6adbe1826614057 files/digest-amap-2.0 223 +RMD160 1b902d1cc9581642a5f47f234de94e2fd5831ab2 files/digest-amap-2.0 223 +SHA256 8c039a4dfb9875f4ca84bb6c15037c6d94a8ac00e20e545f60f1a4eef14cbc93 files/digest-amap-2.0 223 diff --git a/sci-biology/amap/amap-2.0.ebuild b/sci-biology/amap/amap-2.0.ebuild new file mode 100644 index 000000000000..5c681cd0df34 --- /dev/null +++ b/sci-biology/amap/amap-2.0.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2006 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/amap-2.0.ebuild,v 1.1 2006/12/11 06:59:29 dberkholz Exp $ + +inherit eutils toolchain-funcs + +MY_P="${PN}.${PV}" +DESCRIPTION="Protein multiple-alignment-based sequence annealing" +HOMEPAGE="http://bio.math.berkeley.edu/amap/" +SRC_URI="http://bio.math.berkeley.edu/amap/download/${MY_P}.tar.gz" +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~x86" +IUSE="" +RDEPEND="" +DEPEND="${RDEPEND}" +S="${WORKDIR}/${PN}" + +src_unpack() { + unpack ${A} + epatch ${FILESDIR}/${PV}-fix-cxxflags.patch +} + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + OPT_CXXFLAGS="${CXXFLAGS}" \ + || die "make failed" +} + +src_install() { + dobin ${PN} + dodoc README PROBCONS.README +} diff --git a/sci-biology/amap/files/2.0-fix-cxxflags.patch b/sci-biology/amap/files/2.0-fix-cxxflags.patch new file mode 100644 index 000000000000..37155513790d --- /dev/null +++ b/sci-biology/amap/files/2.0-fix-cxxflags.patch @@ -0,0 +1,21 @@ +diff -urN amap.orig/Makefile amap/Makefile +--- amap.orig/Makefile 2006-12-10 22:31:54.000000000 -0800 ++++ amap/Makefile 2006-12-10 22:32:35.000000000 -0800 +@@ -15,6 +15,8 @@ + # c) RELEASE mode + ################################################################################ + ++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops ++ + OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.0"' + + # debug mode +@@ -26,7 +28,7 @@ + + # release mode + #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer +-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops ++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) + + ################################################################################ + # 3) Dependencies diff --git a/sci-biology/amap/files/digest-amap-2.0 b/sci-biology/amap/files/digest-amap-2.0 new file mode 100644 index 000000000000..59ec2916475a --- /dev/null +++ b/sci-biology/amap/files/digest-amap-2.0 @@ -0,0 +1,3 @@ +MD5 48a82988891f210d51f406fb9177f23d amap.2.0.tar.gz 42389 +RMD160 1577da7c930dc72aadda095b24107f933bde4006 amap.2.0.tar.gz 42389 +SHA256 3930c4b5d149f01277bc6de2339c5f058d7d2ca36f69f328f1dac2f1a4b5ba92 amap.2.0.tar.gz 42389 diff --git a/sci-biology/amap/metadata.xml b/sci-biology/amap/metadata.xml new file mode 100644 index 000000000000..34294c65ca04 --- /dev/null +++ b/sci-biology/amap/metadata.xml @@ -0,0 +1,5 @@ + + + +sci-biology + -- 2.26.2