Add mammoth, a nice structural alignment program. It contains the MaxSub algorithm, which is used by lots of people.

Package-Manager: portage-2.1.4_rc4

6 files changed, 126 insertions, 0 deletions

diff --git a/sci-biology/mammoth/ChangeLog b/sci-biology/mammoth/ChangeLog
new file mode 100644
index 000000000000..eef3342c2173
--- /dev/null
+++ b/sci-biology/mammoth/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/mammoth
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mammoth/ChangeLog,v 1.1 2007/12/10 09:11:28 dberkholz Exp $
+
+*mammoth-1.0 (10 Dec 2007)
+
+  10 Dec 2007; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/1.0-consistent-system-intrinsic.patch, +metadata.xml,
+  +mammoth-1.0.ebuild:
+  Add mammoth, a nice structural alignment program. It contains the MaxSub
+  algorithm, which is used by lots of people.
+
diff --git a/sci-biology/mammoth/Manifest b/sci-biology/mammoth/Manifest
new file mode 100644
index 000000000000..3c85ed75e6d5
--- /dev/null
+++ b/sci-biology/mammoth/Manifest
@@ -0,0 +1,30 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 1.0-consistent-system-intrinsic.patch 680 RMD160 71a2feeb7e856d37c5fa7c56e685f29ca1be0eaa SHA1 f0d388f1bea4badd8a127242057d8aeb01c8d974 SHA256 34f47d312af131414154a244218bb4e548d51a3d34b9ed4379c2ec90fba094ca
+MD5 5a8b546609c54dd66d47e23d23e6f878 files/1.0-consistent-system-intrinsic.patch 680
+RMD160 71a2feeb7e856d37c5fa7c56e685f29ca1be0eaa files/1.0-consistent-system-intrinsic.patch 680
+SHA256 34f47d312af131414154a244218bb4e548d51a3d34b9ed4379c2ec90fba094ca files/1.0-consistent-system-intrinsic.patch 680
+DIST mammoth-1.0-src.tgz 319617 RMD160 32b6c9c994ba804fab352cc9cfaa3358784f1052 SHA1 79b5b3ef8873645cf102516df1de7d9b97f206c2 SHA256 7a21bc47db4a47cc5ebeeb4c46761a79eece0a802104a3d6189f388a03e59de2
+EBUILD mammoth-1.0.ebuild 1331 RMD160 928510b1f10053c061c71931b2fb4b74bc7c22e7 SHA1 3edf299bc4936b5b628f99d65fd5da320819cc57 SHA256 b0fc07735b520002de03804b8948e0b597bc56551671d738d9e947fd446e1284
+MD5 ef3263b457d5917e68d3e1d72642bfb8 mammoth-1.0.ebuild 1331
+RMD160 928510b1f10053c061c71931b2fb4b74bc7c22e7 mammoth-1.0.ebuild 1331
+SHA256 b0fc07735b520002de03804b8948e0b597bc56551671d738d9e947fd446e1284 mammoth-1.0.ebuild 1331
+MISC ChangeLog 505 RMD160 3dcf795563bb2289ced1e149443bfd40489dfab6 SHA1 78742b43ecac3dc6af9eb36bf771b839a74b1c8d SHA256 b824b7cc06cc967569e17b2b1069bc68e2af392efee067eef4f57c18f9e8bd0c
+MD5 159a91910e7f17c4e7806e644843d170 ChangeLog 505
+RMD160 3dcf795563bb2289ced1e149443bfd40489dfab6 ChangeLog 505
+SHA256 b824b7cc06cc967569e17b2b1069bc68e2af392efee067eef4f57c18f9e8bd0c ChangeLog 505
+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 9e7286c84db15c55e105c0c055d7c31c files/digest-mammoth-1.0 238
+RMD160 5e825fc810aebb51a230c14a6f8c11e9c81740f4 files/digest-mammoth-1.0 238
+SHA256 a5a779c2a6872f4dcd03544c48302031ea4e3b896bcfc0c8fbe6b8b3370fae56 files/digest-mammoth-1.0 238
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.7 (GNU/Linux)
+
+iD8DBQFHXQLGXVaO67S1rtsRAtkkAKDCI4uanTuHzlyie2q6Sb8O0n404wCgpiQC
+x0JU+S7t3f/ZhVnEugB1JTU=
+=BI8L
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch b/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch
new file mode 100644
index 000000000000..63bf9f246750
--- /dev/null
+++ b/sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch
@@ -0,0 +1,21 @@
+http://gcc.gnu.org/onlinedocs/gcc-4.2.2/gfortran/SYSTEM.html#SYSTEM
+
+This intrinsic is provided in both subroutine and function forms; 
+however, only one form can be used in any given program unit.
+
+--- src/6apply_rot_tras.f.orig	2007-12-10 00:51:35.000000000 -0800
++++ src/6apply_rot_tras.f	2007-12-10 00:55:07.000000000 -0800
+@@ -47,11 +47,11 @@
+       endif
+ 
+ 
+-      call system ('echo $PWD > junk1')
++      i = system ('echo $PWD > junk1')
+       open(unit=21,file='junk1')
+       read(21,'(a340)', end=7) path
+  7    close(21)
+-      call system ('rm -f junk1')
++      i = system ('rm -f junk1')
+ 
+ c      write(6,*)'my path is ', path
+ c      write(6,*)tras1,tras2,tras3,
diff --git a/sci-biology/mammoth/files/digest-mammoth-1.0 b/sci-biology/mammoth/files/digest-mammoth-1.0
new file mode 100644
index 000000000000..3b87d317c321
--- /dev/null
+++ b/sci-biology/mammoth/files/digest-mammoth-1.0
@@ -0,0 +1,3 @@
+MD5 241c7b3ba69974015ea82dad13b5a987 mammoth-1.0-src.tgz 319617
+RMD160 32b6c9c994ba804fab352cc9cfaa3358784f1052 mammoth-1.0-src.tgz 319617
+SHA256 7a21bc47db4a47cc5ebeeb4c46761a79eece0a802104a3d6189f388a03e59de2 mammoth-1.0-src.tgz 319617
diff --git a/sci-biology/mammoth/mammoth-1.0.ebuild b/sci-biology/mammoth/mammoth-1.0.ebuild
new file mode 100644
index 000000000000..5f961af6c5b6
--- /dev/null
+++ b/sci-biology/mammoth/mammoth-1.0.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mammoth/mammoth-1.0.ebuild,v 1.1 2007/12/10 09:11:28 dberkholz Exp $
+
+inherit autotools eutils fortran
+
+MY_P="${P}-src"
+
+DESCRIPTION="MAtching Molecular Models Obtained from THeory"
+HOMEPAGE="http://ub.cbm.uam.es/software.php"
+SRC_URI="${MY_P}.tgz"
+LICENSE="mammoth"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+RESTRICT="fetch"
+RDEPEND=""
+DEPEND="${RDEPEND}"
+S=${WORKDIR}/${MY_P}
+FORTRAN="gfortran g77"
+
+pkg_nofetch() {
+	einfo "Download the source code for MAMMOTH from"
+	einfo "${HOMEPAGE}"
+	einfo "and place it in ${DISTDIR}"
+}
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	# Broken with gfortran without this patch
+	epatch "${FILESDIR}"/${PV}-consistent-system-intrinsic.patch
+
+	case ${FORTRANC} in
+		g77)		append-fflags -ffixed-line-length-none ;;
+		gfortran)	append-fflags -ffixed-line-length-none ;;
+	esac
+
+	# It comes with a custom-modified configure for some reason,
+	# which forces you to pass in the Fortran compiler as a parameter.
+	# Let's do the standard stuff instead.
+	eautoreconf
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die "emake install failed"
+	dodoc README AUTHORS || die
+}
+
+append-fflags() {
+	[[ -z $* ]] && return 0
+	export FFLAGS="${FFLAGS} $*"
+	return 0
+}
diff --git a/sci-biology/mammoth/metadata.xml b/sci-biology/mammoth/metadata.xml
new file mode 100644
index 000000000000..34294c65ca04
--- /dev/null
+++ b/sci-biology/mammoth/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>