proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

1 files changed, 144 insertions, 0 deletions

diff --git a/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
new file mode 100644
index 000000000000..47adf6201db7
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild
@@ -0,0 +1,144 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+	AmberTools-${PV}.tar.bz2
+	mirror://gentoo/${P}-bugfix_1-10.patch.xz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="mpi openmp static-libs 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:2.1
+	sci-chemistry/reduce"
+DEPEND="${RDEPEND}
+	dev-util/byacc
+	dev-libs/libf2c
+	sys-devel/ucpp
+	virtual/pkgconfig"
+S="${WORKDIR}/amber11"
+
+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 \
+		"${WORKDIR}/${P}-bugfix_1-10.patch" \
+		"${FILESDIR}/${P}-gentoo.patch"
+	cd AmberTools/src
+	rm -r arpack blas lapack fftw-2.1.5 c9x-complex cifparse netcdf pnetcdf reduce ucpp-1.3 || die
+}
+
+src_configure() {
+	cd AmberTools/src
+	sed \
+		-e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+		-e "s:\\\\\$(LIBDIR)/lapack.a:$($(tc-getPKG_CONFIG) --libs lapack) -lclapack:g" \
+		-e "s:\\\\\$(LIBDIR)/blas.a:$($(tc-getPKG_CONFIG) --libs blas cblas):g" \
+		-e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+		-e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+		-e "s:CFLAGS=:CFLAGS=${CFLAGS} -DBINTRAJ :g" \
+		-e "s:FFLAGS=:FFLAGS=${FFLAGS} :g" \
+		-e "s:LDFLAGS=$ldflags:LDFLAGS=${LDFLAGS}:g" \
+		-e "s:fc=g77:fc=$(tc-getFC):g" \
+		-e "s:\$netcdflib:$($(tc-getPKG_CONFIG) --libs netcdf):g" \
+		-e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+		-e "s:-O3::g" \
+		-i configure || die
+	sed -e "s:arsecond_:arscnd_:g" \
+		-i sff/time.c \
+		-i sff/sff.h \
+		-i sff/sff.c || die
+	sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \
+		-i nss/Makefile || die
+
+	local myconf
+
+	use X || myconf="${myconf} -noX11"
+
+	for x in mpi openmp; do
+		use ${x} && myconf="${myconf} -${x}"
+	done
+
+	./configure \
+		${myconf} \
+		-nobintraj \
+		-nomdgx \
+		-nopython \
+		-nomtkpp \
+		gnu
+#	$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+}
+
+src_compile() {
+	cd AmberTools/src
+	emake
+}
+
+src_install() {
+	rm -r bin/chemistry bin/MMPBSA_mods
+	rm bin/ante-MMPBSA.py bin/extractFrcmod.py
+	for x in bin/*
+		do dobin ${x} || die
+	done
+	rm "${ED}/usr/bin/yacc"
+	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 "${S}"
+#	sed -e "s:\$AMBERHOME/dat:\$AMBERHOME/share/ambertools/dat:g" \
+#		-i "${ED}/usr/bin/xleap" \
+#		-i "${ED}/usr/bin/tleap" || die
+	dodoc doc/AmberTools.pdf doc/leap_pg.pdf
+
+	use static-libs && dolib.a lib/*
+
+	insinto /usr/include/${PN}
+	doins include/*
+
+	insinto /usr/share/${PN}
+	doins -r dat
+
+	cd AmberTools
+	doins -r benchmarks examples test
+
+	cat >> "${T}"/99ambertools <<- EOF
+	AMBERHOME="${EPREFIX}/usr/share/ambertools"
+	EOF
+	doenvd "${T}"/99ambertools
+}