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author | 2009-07-11 17:55:38 -0700 | |
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committer | 2009-07-11 17:55:38 -0700 | |
commit | 4678d9ff21fc3e37bf28f3a33bb43353fd62963a (patch) | |
tree | 24dedeac9f790820b3117517846e86f477670952 /sci-chemistry | |
parent | syslog-ng: bump to 3.0.3 (diff) | |
download | dberkholz-4678d9ff21fc3e37bf28f3a33bb43353fd62963a.tar.gz dberkholz-4678d9ff21fc3e37bf28f3a33bb43353fd62963a.tar.bz2 dberkholz-4678d9ff21fc3e37bf28f3a33bb43353fd62963a.zip |
mustang: bump to 3.2
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/mustang/ChangeLog | 25 | ||||
-rw-r--r-- | sci-chemistry/mustang/Manifest | 5 | ||||
-rw-r--r-- | sci-chemistry/mustang/files/mustang-3-gcc43.patch | 55 | ||||
-rw-r--r-- | sci-chemistry/mustang/metadata.xml | 5 | ||||
-rw-r--r-- | sci-chemistry/mustang/mustang-3.2.ebuild | 42 |
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" +} |