Initial commit

Package-Manager: portage-2.2_rc12/cvs/Linux 2.6.26-tuxonice i686

6 files changed, 109 insertions, 0 deletions

diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog
new file mode 100644
index 000000000000..0ce7baab6336
--- /dev/null
+++ b/sci-biology/augustus/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/augustus
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.1 2009/01/04 00:26:13 weaver Exp $
+
+*augustus-2.0.3 (04 Jan 2009)
+
+  04 Jan 2009; weaver <weaver@gentoo.org>
+  +files/augustus-2.0.3-cflags.patch, +files/augustus-2.0.3-gcc4.3.patch,
+  +metadata.xml, +augustus-2.0.3.ebuild:
+  Initial commit, ebuild written by me
+
diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest
new file mode 100644
index 000000000000..edfd67547067
--- /dev/null
+++ b/sci-biology/augustus/Manifest
@@ -0,0 +1,6 @@
+AUX augustus-2.0.3-cflags.patch 646 RMD160 a83852c8520ac12782dfe114fbd7618ce732bdc7 SHA1 1ee661682a11b99178ed77f1dec23b6241d2e8e7 SHA256 ef50cdbce090aa8404fd48ab98de2ab9bfe239bf352914bee3eceea3f466e87e
+AUX augustus-2.0.3-gcc4.3.patch 726 RMD160 1d6df43e6dd96c365bd3a0ca17136b13d38a789e SHA1 42bb3c4f1d9dcb4ebf5bd1c4fc6f2464cd62230c SHA256 c548b0ed5d63c9e81e6ebf8dd799bdbccb5096350b0d6253129d0529fb55defa
+DIST augustus.2.0.3.src.tar.gz 24488810 RMD160 6cb81134a6e554f3e9e436ebc8c9de0cc80e4d58 SHA1 c4039781493f2de6e507a6afb80b8393e60e8155 SHA256 b0964585247eae16752db17fc7d7b89667edb928dde53119ceb7dde265a696e5
+EBUILD augustus-2.0.3.ebuild 828 RMD160 6f0df726c96f8c92883682cb9dfa5c2d688963c2 SHA1 73f70ab5f96a6a2ea5a5e54ed9d2faa6900ebdbf SHA256 6bdb1bcefe48ad606d49af22673f0d6ee246dd32b0f2d188f0f1d8a827a5c243
+MISC ChangeLog 441 RMD160 474ab0b70b8f7859a5262e87fe25d7ec16ef78aa SHA1 1e29b2b0878d44b31e6e8b49587b68c06ff5f013 SHA256 4c3c263b59dd6faf9f2c5592455d34709ff4b5670116321b494060e7f8a6e5f4
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/augustus/augustus-2.0.3.ebuild b/sci-biology/augustus/augustus-2.0.3.ebuild
new file mode 100644
index 000000000000..44828a0c4745
--- /dev/null
+++ b/sci-biology/augustus/augustus-2.0.3.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.0.3.ebuild,v 1.1 2009/01/04 00:26:13 weaver Exp $
+
+inherit eutils
+
+DESCRIPTION="Eukaryotic gene predictor"
+HOMEPAGE="http://augustus.gobics.de/"
+SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.src.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/${PN}"
+
+src_unpack() {
+	unpack ${A}
+	epatch "${FILESDIR}"/${P}-*.patch
+}
+
+src_compile() {
+	emake -C src
+}
+
+src_install() {
+	dobin src/{augustus,etraining}
+	insinto /usr/share/${PN}
+	doins -r config examples scripts
+	echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
+	doenvd "${S}/99${PN}"
+	dodoc README.TXT HISTORY.TXT
+}
diff --git a/sci-biology/augustus/files/augustus-2.0.3-cflags.patch b/sci-biology/augustus/files/augustus-2.0.3-cflags.patch
new file mode 100644
index 000000000000..203e100a313e
--- /dev/null
+++ b/sci-biology/augustus/files/augustus-2.0.3-cflags.patch
@@ -0,0 +1,20 @@
+diff -rc augustus.orig/src/Makefile augustus/src/Makefile
+*** augustus.orig/src/Makefile	2009-01-03 18:26:17.000000000 -0500
+--- augustus/src/Makefile	2009-01-03 18:38:35.000000000 -0500
+***************
+*** 3,9 ****
+  #
+  
+  CC	= g++
+! CFLAGS	= -Wall -ansi -pedantic -O2 -g -ggdb # -O2 -g -pg -ggdb -DDEBUG -static -DDEBUG  -pg
+  INCLS	= -I../include -I.
+  LIBS	= # -lcwd
+  OBJS	= genbank.o properties.o statemodel.o \
+--- 3,9 ----
+  #
+  
+  CC	= g++
+! CFLAGS	:= -Wall -ansi -pedantic -O2 -g -ggdb ${CFLAGS} # -O2 -g -pg -ggdb -DDEBUG -static -DDEBUG  -pg
+  INCLS	= -I../include -I.
+  LIBS	= # -lcwd
+  OBJS	= genbank.o properties.o statemodel.o \
diff --git a/sci-biology/augustus/files/augustus-2.0.3-gcc4.3.patch b/sci-biology/augustus/files/augustus-2.0.3-gcc4.3.patch
new file mode 100644
index 000000000000..8f6dc33ad276
--- /dev/null
+++ b/sci-biology/augustus/files/augustus-2.0.3-gcc4.3.patch
@@ -0,0 +1,26 @@
+diff -rc augustus.orig/include/help.hh augustus/include/help.hh
+*** augustus.orig/include/help.hh	2009-01-03 18:26:17.000000000 -0500
+--- augustus/include/help.hh	2009-01-03 18:36:30.000000000 -0500
+***************
+*** 23,28 ****
+--- 23,29 ----
+  #include <cmath>
+  #include <cstring>
+  #include <cctype>
++ #include <stdlib.h>
+  
+  #include "types.hh"
+  #include "projecterror.hh"
+diff -rc augustus.orig/include/types.hh augustus/include/types.hh
+*** augustus.orig/include/types.hh	2009-01-03 18:26:17.000000000 -0500
+--- augustus/include/types.hh	2009-01-03 18:36:39.000000000 -0500
+***************
+*** 21,26 ****
+--- 21,27 ----
+  #define _TYPES_HH
+  
+  #include <string>
++ #include <limits.h>
+  
+  #include "lldouble.hh"
+  
diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/augustus/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>