ambertools: Version bump to 12

sci-chemistry/ambertools/ChangeLog

@@ -2,6 +2,12 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
+*ambertools-12 (20 Oct 2012)
+
+  20 Oct 2012; Reinis Danne <rei4dan@gmail.com> +ambertools-12.ebuild,
+  +files/ambertools-12-bugfix_14-26.patch, +files/ambertools-12-gentoo.patch:
+  Bump to 12.
+
 *ambertools-1.5-r4 (28 Aug 2012)
 
   28 Aug 2012; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5-r4.ebuild,

sci-chemistry/ambertools/Manifest

@@ -1 +1,2 @@
 DIST AmberTools-1.5.tar.bz2 121062582 SHA256 0c7d397d2e91603bb9123ae68e91af3525269e60800ced360f68c13350651d7c SHA512 3366bfe6d0ee1f9b5b99b1d6aad4111093919fe43ab5e9753c62ae815dca958bfc660a3af9db83de71690624869ee5e47af51a6c8412c6bdcb32aecbefb01677 WHIRLPOOL 192f027f5480807cd36693c6c7d8e3b809f4032ecb1a1bf97df888bd02974fbd2bc8da4ea0e9d52062dce10e969bb72cc2f1ba9c4d627f6097492175ab025120
+DIST AmberTools12.tar.bz2 89175545 SHA256 aff5dbc29b5b5b29a85ae465d3e250e225cd85deb2bce828833c2dc769e81009 SHA512 4c34d460fdedf00ade847040856d4bf7df65e7370d4a696dd858fdd3612c192ddc13dabde559bc1a7ae4068ba8040ee159479e247b2c1e59ed976a5aa6344970 WHIRLPOOL 3bc134875482d00d0d1861e9d87f4fef9fdebd1f6860b2c4623f48c23f6f8673df4b23069f3e9374ef9814d500f23f986250a1bcae093597c9e0a0c9d40d6c86

sci-chemistry/ambertools/ambertools-12.ebuild

@@ -0,0 +1,151 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+	AmberTools${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="openmp X"
+
+RESTRICT="fetch"
+
+RDEPEND="
+	virtual/cblas
+	virtual/lapack
+	sci-libs/clapack
+	sci-libs/arpack
+	sci-libs/cifparse-obj
+	sci-chemistry/mopac7
+	sci-libs/netcdf
+	sci-libs/fftw:3.0
+	sci-chemistry/reduce"
+DEPEND="${RDEPEND}
+	app-shells/tcsh
+	dev-util/byacc
+	dev-libs/libf2c
+	sys-devel/ucpp"
+
+S="${WORKDIR}/amber12"
+
+pkg_nofetch() {
+	einfo "Go to ${HOMEPAGE} and get ${A}"
+	einfo "Place it in ${DISTDIR}"
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	if use openmp; then
+		tc-has-openmp || \
+			die "Please select an openmp capable compiler like gcc[openmp]"
+	fi
+	AMBERHOME="${S}"
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}/${P}-bugfix_14-26.patch" \
+		"${FILESDIR}/${P}-gentoo.patch"
+	cd "${S}"/AmberTools/src
+	rm -r \
+		arpack \
+		blas \
+		byacc \
+		lapack \
+		fftw-3.3 \
+		c9x-complex \
+		cifparse \
+		netcdf \
+		reduce \
+		ucpp-1.3 \
+		|| die
+}
+
+src_configure() {
+	cd "${S}"/AmberTools/src
+	sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+		-e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
+		-e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
+		-e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
+		-e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
+		-e "s:GENTOO_INCLUDE:${EPREFIX}/usr/include:g" \
+		-e "s:GENTOO_FFTW3_LIBS:$(pkg-config fftw3 --libs):" \
+		-e "s:fc=g77:fc=$(tc-getFC):g" \
+		-e "s:\$netcdfflag:$(pkg-config netcdf --libs):g" \
+		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+		-i configure2 || die
+	sed -e "s:arsecond_:arscnd_:g" \
+		-i sff/time.c \
+		-i sff/sff.h \
+		-i sff/sff.c || die
+
+	local myconf="--no-updates"
+
+	use X || myconf="${myconf} -noX11"
+
+	use openmp && myconf="${myconf} -openmp"
+
+	cd "${S}"
+	./configure \
+		${myconf} \
+		-nobintraj \
+		-nomtkpp \
+		gnu
+}
+
+src_compile() {
+	cd "${S}"/AmberTools/src
+	emake
+}
+
+src_test() {
+	cd "${S}"/AmberTools/test
+	emake test
+}
+
+src_install() {
+	rm bin/*.py
+
+	for x in bin/*
+	do
+		[ ! -d ${x} ] && dobin ${x}
+	done
+
+	dobin AmberTools/src/antechamber/mopac.sh
+	sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+		-i "${ED}/usr/bin/mopac.sh" || die
+
+	# Make symlinks untill binpath for amber will be fixed
+	dodir /usr/share/${PN}/bin
+	cd "${ED}/usr/bin"
+	for x in *
+		do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
+	done
+	cd "${S}"
+
+	dodoc doc/AmberTools12.pdf
+	dolib.a lib/*
+	insinto /usr/include/${PN}
+	doins include/*
+	insinto /usr/share/${PN}
+	doins -r dat
+	cd AmberTools
+	doins -r benchmarks
+	doins -r examples
+	doins -r test
+
+	cat >> "${T}"/99ambertools <<- EOF
+	AMBERHOME="${EPREFIX}/usr/share/ambertools"
+	EOF
+	doenvd "${T}"/99ambertools
+}