mustang: bump to 3.2

5 files changed, 132 insertions, 0 deletions

diff --git a/sci-chemistry/mustang/ChangeLog b/sci-chemistry/mustang/ChangeLog
new file mode 100644
index 0000000..befb97d
--- /dev/null
+++ b/sci-chemistry/mustang/ChangeLog
@@ -0,0 +1,25 @@
+# ChangeLog for sci-chemistry/mustang
+# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mustang/ChangeLog,v 1.5 2008/12/19 20:22:42 loki_val Exp $
+
+  19 Dec 2008; Peter Alfredsen <loki_val@gentoo.org>
+  +files/mustang-3-gcc43.patch, mustang-3.ebuild:
+  Fix bug 250420 thanks to Joel <joel_123@hotmail.com>
+
+  29 Apr 2008; Markus Dittrich <markusle@gentoo.org> ChangeLog:
+  Redigested ebuild to fix broken Manifest (bug #219429).
+
+  11 Dec 2006; Donnie Berkholz <dberkholz@gentoo.org>; mustang-3.ebuild:
+  Stable on x86.
+
+  11 Dec 2006; Donnie Berkholz <dberkholz@gentoo.org>; mustang-3.ebuild:
+  License is more accurately the generic BSD than the specific Intel (although
+  perhaps that shouldn't even exist); also add reference for citation (Arun S.
+  Konagurthu).
+
+*mustang-3 (21 Oct 2006)
+
+  21 Oct 2006; Donnie Berkholz <dberkholz@gentoo.org>; +metadata.xml,
+  +mustang-3.ebuild:
+  New package: MUltiple STructural AligNment AlGorithm.
+
diff --git a/sci-chemistry/mustang/Manifest b/sci-chemistry/mustang/Manifest
new file mode 100644
index 0000000..f382405
--- /dev/null
+++ b/sci-chemistry/mustang/Manifest
@@ -0,0 +1,5 @@
+AUX mustang-3-gcc43.patch 2262 RMD160 d2f9d6de98f679af3b15507b42a410f1e0ba7e08 SHA1 532517644ceaaa0e4263cb04e78f3f47df450592 SHA256 2d9ec5f36d069e51909d56a58003c51bcd409c78946712753d313192c48558b2
+DIST mustang_v3.2.tgz 160663 RMD160 5486c7037725e32d999a4d938c532e5808b3e9c3 SHA1 23897b36af7a682cee470a5feff77f5e9488c631 SHA256 e8b16a1ce95f40fe77f10e0c6cf1f1e8eaf6f4274c76b9508bc4e3f41dcd86b0
+EBUILD mustang-3.2.ebuild 1079 RMD160 6ef522e44b46194ffe80a112564a3d6893a07dde SHA1 23b5e6fdc5f655093a8658cf7b95a58a7a24ed66 SHA256 d2ae8a72f17e697bb62cffe13a0eb4f387030a498e2522cb5f888e6570d8041e
+MISC ChangeLog 1011 RMD160 58e24b4585bf7bfabee3572aae147f1ae9112b7f SHA1 77d8d59f960271506afcbb3e673b6270062de0fd SHA256 c4ff86829ae8bf7bcc93118e7f5f9ab01bb48ed8f1d7614218d1f0a132c6deea
+MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/mustang/files/mustang-3-gcc43.patch b/sci-chemistry/mustang/files/mustang-3-gcc43.patch
new file mode 100644
index 0000000..ef2818b
--- /dev/null
+++ b/sci-chemistry/mustang/files/mustang-3-gcc43.patch
@@ -0,0 +1,55 @@
+diff -u MUSTANG_v.3.orig/src/ew_2.cpp MUSTANG_v.3/src/ew_2.cpp
+--- MUSTANG_v.3.orig/src/ew_2.cpp	2008-01-15 11:18:34.000000000 -0700
++++ MUSTANG_v.3/src/ew_2.cpp	2008-12-09 10:47:22.000000000 -0700
+@@ -36,6 +36,7 @@
+ using std::ifstream;
+ 
+ #include<math.h>
++#include <cstdlib>
+ #include "macros.h"
+ #include "globals.h"
+ #include "ew.h"
+diff -u MUSTANG_v.3.orig/src/multiple_superposition.cpp MUSTANG_v.3/src/multiple_superposition.cpp
+--- MUSTANG_v.3.orig/src/multiple_superposition.cpp	2008-01-15 11:18:34.000000000 -0700
++++ MUSTANG_v.3/src/multiple_superposition.cpp	2008-12-09 10:49:00.000000000 -0700
+@@ -51,6 +51,7 @@
+ #include "alloc_routines.h"
+ #include "de_alloc_routines.h"
+ #include <cmath>
++#include <cstdlib>
+ #define THRESH 0.0001
+ 
+ void MOVE_TO_CENTER_OF_GRAVITY( int NSTRUC , int NRES , float ***R , float **CMs )
+diff -u MUSTANG_v.3.orig/src/multiple_superposition.h MUSTANG_v.3/src/multiple_superposition.h
+--- MUSTANG_v.3.orig/src/multiple_superposition.h	2008-01-15 11:18:34.000000000 -0700
++++ MUSTANG_v.3/src/multiple_superposition.h	2008-12-09 10:48:11.000000000 -0700
+@@ -25,3 +25,4 @@
+ #define MULT_SUPERPOSE
+ void  M_SUPERPOSE( int , int , float***, float** , float*** ) ;
+ #endif
++#include <cstdlib>
+diff -u MUSTANG_v.3.orig/src/pdb_ripper.h MUSTANG_v.3/src/pdb_ripper.h
+--- MUSTANG_v.3.orig/src/pdb_ripper.h	2008-01-15 11:18:34.000000000 -0700
++++ MUSTANG_v.3/src/pdb_ripper.h	2008-12-09 10:46:47.000000000 -0700
+@@ -29,4 +29,5 @@
+ void PARSE_ENTIRE_PDB_STRUCTURE( char * , int ) ;
+ 
+ #endif
++#include <cstdlib>
+ 
+diff -u MUSTANG_v.3.orig/src/progress_align.h MUSTANG_v.3/src/progress_align.h
+--- MUSTANG_v.3.orig/src/progress_align.h	2008-01-15 11:18:34.000000000 -0700
++++ MUSTANG_v.3/src/progress_align.h	2008-12-09 10:47:50.000000000 -0700
+@@ -25,3 +25,4 @@
+ #define PROG_ALGN_H
+ void PROGRESSIVE_ALIGNMENT_USING_EXTENDED_EDGE_WEIGHTS() ;
+ #endif
++#include <cstdlib>
+diff -u MUSTANG_v.3.orig/src/read_structures.h MUSTANG_v.3/src/read_structures.h
+--- MUSTANG_v.3.orig/src/read_structures.h	2008-01-15 11:18:34.000000000 -0700
++++ MUSTANG_v.3/src/read_structures.h	2008-12-09 10:46:22.000000000 -0700
+@@ -26,3 +26,4 @@
+ void READ_STRUCTURES( char **paths );
+ void READ_ENTIRE_PDBS( char **paths) ;
+ #endif
++#include <cstdlib>
diff --git a/sci-chemistry/mustang/metadata.xml b/sci-chemistry/mustang/metadata.xml
new file mode 100644
index 0000000..9ac9ffd
--- /dev/null
+++ b/sci-chemistry/mustang/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-chemistry</herd>
+</pkgmetadata>
diff --git a/sci-chemistry/mustang/mustang-3.2.ebuild b/sci-chemistry/mustang/mustang-3.2.ebuild
new file mode 100644
index 0000000..47de106
--- /dev/null
+++ b/sci-chemistry/mustang/mustang-3.2.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mustang/mustang-3.ebuild,v 1.4 2008/12/19 20:22:42 loki_val Exp $
+
+inherit base toolchain-funcs
+
+MY_PN="MUSTANG"
+SRC_P="${PN}_v${PV}"
+MY_P="${MY_PN}_v${PV}"
+DESCRIPTION="MUltiple STructural AligNment AlGorithm."
+HOMEPAGE="http://www.cs.mu.oz.au/~arun/mustang/"
+SRC_URI="${HOMEPAGE}${SRC_P}.tgz"
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="x86 ~amd64"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}"
+S="${WORKDIR}/${MY_P}"
+
+src_compile() {
+	emake \
+		CPP=$(tc-getCXX) \
+		CPPFLAGS="${CXXFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		|| die "emake failed"
+}
+
+src_test() {
+	./bin/MUSTANG_v.${PV} -f ./data/test/test_zf-CCHH
+}
+
+src_install() {
+	newbin bin/MUSTANG_v.3 mustang
+	doman man/mustang.1
+}
+
+pkg_postinst() {
+	elog "If you use this program for an academic paper, please cite:"
+	elog "Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey, and Arthur M. Lesk"
+	elog "Proteins: Structure, Function, and Bioinformatics. 64(3):559-574, Aug. 2006"
+}