New package: Protein multiple-alignment-based sequence annealing. It's based on ProbCons and adds sequence annealing. See the homepage for details.

(Portage version: 2.1.2_rc3-r1)

6 files changed, 94 insertions, 0 deletions

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 <dberkholz@gentoo.org>;
+  +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..9857d67797b1
--- /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 810 RMD160 a52bca0fd4142ccb5e775234bd27dfeecc60add5 SHA1 1c0964f0593f2a1a3a795ed0c82c77aeef04fb61 SHA256 92b3209efb0b80d3d31962ff0aea0ca93b66bcc7ad3c203c845f174761435e45
+MD5 0b24097576b160b05e594ab5398e1dd9 amap-2.0.ebuild 810
+RMD160 a52bca0fd4142ccb5e775234bd27dfeecc60add5 amap-2.0.ebuild 810
+SHA256 92b3209efb0b80d3d31962ff0aea0ca93b66bcc7ad3c203c845f174761435e45 amap-2.0.ebuild 810
+MISC ChangeLog 416 RMD160 5a390f53c2165501374894d7534fb2d08595c519 SHA1 4c3c18641e6002afa7b15f2ed8b2c985e43c687b SHA256 8dd7f819b4bf96498020b6b1e0c9a3b6f6356a54ea69b49168c4c90272498069
+MD5 c3f93ff2fd75651203c3712557e768ad ChangeLog 416
+RMD160 5a390f53c2165501374894d7534fb2d08595c519 ChangeLog 416
+SHA256 8dd7f819b4bf96498020b6b1e0c9a3b6f6356a54ea69b49168c4c90272498069 ChangeLog 416
+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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+</pkgmetadata>