New package: Fast multiple sequence alignments using partial-order graphs.

Package-Manager: portage-2.1.2_pre3-r5

6 files changed, 95 insertions, 0 deletions

diff --git a/sci-biology/poa/ChangeLog b/sci-biology/poa/ChangeLog
new file mode 100644
index 000000000000..0a22d78bc44b
--- /dev/null
+++ b/sci-biology/poa/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/poa
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/poa/ChangeLog,v 1.1 2006/10/21 06:31:50 dberkholz Exp $
+
+*poa-2 (21 Oct 2006)
+
+  21 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/respect-cflags.patch, +metadata.xml, +poa-2.ebuild:
+  New package: Fast multiple sequence alignments using partial-order graphs.
+
diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest
new file mode 100644
index 000000000000..3878f5e100aa
--- /dev/null
+++ b/sci-biology/poa/Manifest
@@ -0,0 +1,20 @@
+AUX respect-cflags.patch 464 RMD160 c5323a4944cc953336b70f924ced36aca1533301 SHA1 e6ed80baa01ed807778411760b69e51e969b9601 SHA256 851c738b9ecfa567b21f3b551e6819b8ae05db02a3f5a42ae4aa93d55577ed0e
+MD5 bed0da2f6883825c195e05f8f00e5415 files/respect-cflags.patch 464
+RMD160 c5323a4944cc953336b70f924ced36aca1533301 files/respect-cflags.patch 464
+SHA256 851c738b9ecfa567b21f3b551e6819b8ae05db02a3f5a42ae4aa93d55577ed0e files/respect-cflags.patch 464
+DIST poaV2.tar.gz 62612 RMD160 31fdc50527a826fb7fdab4256f51e4f0f03c5492 SHA1 57f863956736498dd76afb57967036bf92c6d599 SHA256 d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2
+EBUILD poa-2.ebuild 1056 RMD160 2c9c47ee0a20e79f5a181fa168b9379e9fd02eb4 SHA1 ade25dedae2213a95d46dfce88fb27b0a4af0af2 SHA256 c9a0c0ad1a5e294e558591fa452cd5998d2d033806607ff525c21389fc8ff0a0
+MD5 5fb4053442096e8eda2497cf01156e6d poa-2.ebuild 1056
+RMD160 2c9c47ee0a20e79f5a181fa168b9379e9fd02eb4 poa-2.ebuild 1056
+SHA256 c9a0c0ad1a5e294e558591fa452cd5998d2d033806607ff525c21389fc8ff0a0 poa-2.ebuild 1056
+MISC ChangeLog 422 RMD160 770686bae251d6612a9abf66ac81b91aff8c4eb0 SHA1 a47cde8c95150eef1929f97d670f1a62669d3faf SHA256 435a2fa8efe7d7b6ff0f118a7003fe878a226565a765e7387eaa8f1e041726aa
+MD5 6e4e2b441c598d9c2d96a61c360af0ed ChangeLog 422
+RMD160 770686bae251d6612a9abf66ac81b91aff8c4eb0 ChangeLog 422
+SHA256 435a2fa8efe7d7b6ff0f118a7003fe878a226565a765e7387eaa8f1e041726aa ChangeLog 422
+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 c40b5662c1ced482b5071f596493c297 files/digest-poa-2 214
+RMD160 ca39533967c38989bfc8b08772a53dba3d09ce15 files/digest-poa-2 214
+SHA256 034b82fef594cbf7567ceca3fa49e761d5b1654df48056be2d708d63f792127a files/digest-poa-2 214
diff --git a/sci-biology/poa/files/digest-poa-2 b/sci-biology/poa/files/digest-poa-2
new file mode 100644
index 000000000000..acdb4416cb4e
--- /dev/null
+++ b/sci-biology/poa/files/digest-poa-2
@@ -0,0 +1,3 @@
+MD5 9e2eb270d4867114406f53dab1311b2b poaV2.tar.gz 62612
+RMD160 31fdc50527a826fb7fdab4256f51e4f0f03c5492 poaV2.tar.gz 62612
+SHA256 d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2 poaV2.tar.gz 62612
diff --git a/sci-biology/poa/files/respect-cflags.patch b/sci-biology/poa/files/respect-cflags.patch
new file mode 100644
index 000000000000..2ae08db4ff4d
--- /dev/null
+++ b/sci-biology/poa/files/respect-cflags.patch
@@ -0,0 +1,13 @@
+diff -urN poaV2.orig/Makefile poaV2/Makefile
+--- poaV2.orig/Makefile	2004-03-11 21:33:30.000000000 -0800
++++ poaV2/Makefile	2006-03-09 20:09:27.000000000 -0800
+@@ -28,7 +28,8 @@
+ 
+ CC = gcc
+ #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
++OPT_CFLAGS = -g
++CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+ # -I$(HOME)/lib/include
+ # -DREPORT_MAX_ALLOC
+ 
diff --git a/sci-biology/poa/metadata.xml b/sci-biology/poa/metadata.xml
new file mode 100644
index 000000000000..34294c65ca04
--- /dev/null
+++ b/sci-biology/poa/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>
diff --git a/sci-biology/poa/poa-2.ebuild b/sci-biology/poa/poa-2.ebuild
new file mode 100644
index 000000000000..d067811fa64a
--- /dev/null
+++ b/sci-biology/poa/poa-2.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/poa/poa-2.ebuild,v 1.1 2006/10/21 06:31:50 dberkholz Exp $
+
+inherit eutils
+
+MY_P="${PN}V${PV}"
+DESCRIPTION="Fast multiple sequence alignments using partial-order graphs"
+HOMEPAGE="http://www.bioinformatics.ucla.edu/poa/"
+SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz"
+# According to SF project page
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}"
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	epatch "${FILESDIR}"/respect-cflags.patch
+}
+
+src_compile() {
+	emake \
+		OPT_CFLAGS="${CFLAGS}" \
+		poa \
+		|| die "make failed"
+}
+
+src_install() {
+	exeinto /usr/bin
+	doexe "${S}"/poa "${S}"/make_pscores.pl
+	dolib.a "${S}"/liblpo.a
+	dodoc "${S}"/README "${S}"/multidom.*
+	insinto /usr/share/poa
+	doins "${S}"/*.mat
+}
+
+pkg_postinst() {
+	elog "poa requires a score matrix as the first argument."
+	elog "This package installs two examples to ${ROOT}usr/share/poa/."
+}