From 81ca6704b6681e4d0fc343d546ef581e2d2dc53c Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Tue, 27 Oct 2015 10:53:09 +0100 Subject: sci-chemistry/mustang: Version Bump Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher --- sci-chemistry/mustang/Manifest | 1 + sci-chemistry/mustang/files/mustang-3-gcc43.patch | 55 ----------------------- sci-chemistry/mustang/mustang-3.2.2.ebuild | 50 +++++++++++++++++++++ 3 files changed, 51 insertions(+), 55 deletions(-) delete mode 100644 sci-chemistry/mustang/files/mustang-3-gcc43.patch create mode 100644 sci-chemistry/mustang/mustang-3.2.2.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/mustang/Manifest b/sci-chemistry/mustang/Manifest index 278238854069..f8d1b591405d 100644 --- a/sci-chemistry/mustang/Manifest +++ b/sci-chemistry/mustang/Manifest @@ -1 +1,2 @@ DIST mustang_v3.2.1.tgz 161216 SHA256 38f8ec10f15466a42ade770eb6c3ed0ed2449bb070a53b5e8d3125f2596b1556 SHA512 aee37bb77edbdc601cdc735db8602d0a3804065200df1b36b6956e74dfd5f85b554a655be1bfbe673aada1abd5e1aee1c0f59fb2ff0380bfcb725e38439d41ff WHIRLPOOL 521edce7648c28c067dae4462e432c8b5f2b9a60be4248ba78280067254fdfb9f584c18ce9afc5c99927f6227e1e650989cd7d65df1b3c6e7494d617b89a74fe +DIST mustang_v3.2.2.tgz 141940 SHA256 6fe274a93b54ba3c46e262fc6d7114bad239d1cbd2dadec8a92a7194328373a2 SHA512 cb862f860f3cdb3349743c6005a29acc14cde5269df9d61f1100ffdc9a22c1d8e3dd46771371557b823724e79783f8fcb7356c63c6f0c0a09aac09bee407a26d WHIRLPOOL 63e7b6f881274c20df59e85699b1f1a07506f0dd20082e898001c163fb02b60336c0ee6b629bf19f773f86b3479f4ae1344cf1ea6b7f6052d1407db3f05910bb diff --git a/sci-chemistry/mustang/files/mustang-3-gcc43.patch b/sci-chemistry/mustang/files/mustang-3-gcc43.patch deleted file mode 100644 index ef2818b92ed8..000000000000 --- a/sci-chemistry/mustang/files/mustang-3-gcc43.patch +++ /dev/null @@ -1,55 +0,0 @@ -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 -+#include - #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 -+#include - #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 -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 - -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 -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 diff --git a/sci-chemistry/mustang/mustang-3.2.2.ebuild b/sci-chemistry/mustang/mustang-3.2.2.ebuild new file mode 100644 index 000000000000..fdc300fd2b0b --- /dev/null +++ b/sci-chemistry/mustang/mustang-3.2.2.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils toolchain-funcs + +MY_PN="MUSTANG" +SRC_P="${PN}_v${PV}" +MY_P="${MY_PN}_v${PV}" + +DESCRIPTION="MUltiple STructural AligNment AlGorithm" +HOMEPAGE="http://www.csse.monash.edu.au/~karun/Site/mustang.html" +SRC_URI="http://www.csse.monash.edu.au/~karun/${PN}/${PN}_v${PV}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-3.2.1-gcc-4.7.patch + sed -e 's:3.2.1:3.2.2:g' -i Makefile || die +} + +src_compile() { + emake \ + CPP=$(tc-getCXX) \ + CPPFLAGS="${CXXFLAGS}" \ + LDFLAGS="${LDFLAGS}" +} + +src_test() { + ./bin/${P} -f ./data/test/test_zf-CCHH || die +} + +src_install() { + newbin bin/${P} ${PN} + doman man/${PN}.1 + dodoc README +} + +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" +} -- cgit v1.2.3