From bf9a7d687aef8a75cc894dfb2210c3f32883b070 Mon Sep 17 00:00:00 2001 From: Donnie Berkholz Date: Mon, 10 Dec 2007 09:11:28 +0000 Subject: 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 --- sci-biology/mammoth/ChangeLog | 12 +++++ sci-biology/mammoth/Manifest | 30 ++++++++++++ .../files/1.0-consistent-system-intrinsic.patch | 21 +++++++++ sci-biology/mammoth/files/digest-mammoth-1.0 | 3 ++ sci-biology/mammoth/mammoth-1.0.ebuild | 55 ++++++++++++++++++++++ sci-biology/mammoth/metadata.xml | 5 ++ 6 files changed, 126 insertions(+) create mode 100644 sci-biology/mammoth/ChangeLog create mode 100644 sci-biology/mammoth/Manifest create mode 100644 sci-biology/mammoth/files/1.0-consistent-system-intrinsic.patch create mode 100644 sci-biology/mammoth/files/digest-mammoth-1.0 create mode 100644 sci-biology/mammoth/mammoth-1.0.ebuild create mode 100644 sci-biology/mammoth/metadata.xml (limited to 'sci-biology') 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 ; + +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 @@ + + + +sci-biology + -- cgit v1.2.3-65-gdbad