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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
inherit flag-o-matic fortran-2 toolchain-funcs
DESCRIPTION="System for chemical shifts based protein structure prediction using ROSETTA"
HOMEPAGE="http://spin.niddk.nih.gov/bax/software/CSROSETTA/"
SRC_URI="
http://spin.niddk.nih.gov/bax/software/CSROSETTA/install.com -> ${P}-install.com
http://spin.niddk.nih.gov/bax/software/CSROSETTA/CSRosetta.tar.Z -> ${P}.tar.Z
http://spin.niddk.nih.gov/bax/software/CSROSETTA/changeLog -> ${P}-changelog"
SLOT="0"
LICENSE="all-rights-reserved"
KEYWORDS="~x86 ~amd64-linux ~x86-linux"
IUSE="custom-cflags"
RDEPEND="
dev-lang/perl
|| ( sci-biology/update-blastdb sci-biology/ncbi-tools++ )
sci-biology/profphd
sci-biology/psipred
sci-biology/samtools
~sci-libs/cs-rosetta-db-${PV}
sci-chemistry/nmrpipe
sci-chemistry/rosetta"
DEPEND=""
S="${WORKDIR}"
src_unpack() {
unpack ${P}.tar.Z
}
src_prepare() {
cat >> "${T}"/39${PN} <<- EOF
rosetta3="${EPREFIX}/usr/bin/AbinitioRelax"
rosetta3_extpdbs="${EPREFIX}/usr/bin/extract_pdbs"
rosetta3DB="${EPREFIX}/usr/share/rosetta-db"
csrosettaDir="${EPREFIX}/opt/${PN}"
csrosettaCom="${EPREFIX}/opt/${PN}/com"
PATH="${EPREFIX}/opt/${PN}/com"
MFR="${EPREFIX}/opt/${PN}/com/mfr.tcl"
EOF
# needs more love
sed \
-e "s:CSROSETTA_DIR/src/nnmake/pNNMAKE.gnu:${EPREFIX}/opt/${PN}/src/nnmake/pNNMAKE:g" \
-i com/make_fragments_2000.pl || die
append-fflags -ffixed-line-length-132
}
src_compile() {
use custom-cflags || CXXFLAGS="-pipe -ffor-scope -fno-exceptions -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000"
compilation() {
if [[ -f dipolar_nn.f ]]; then
sed \
-e '/write/s:(i,6f6.3):(i3,6(1x,f6.3)):g' \
-i dipolar_nn.f || die
fi
sed \
-e '/LDFLAGS/s: = : ?= :g' \
-e '/CCFLAGS/s: = : += :g' \
-e 's:$(OBJECT) $(LDFLAGS):$(LDFLAGS) $(OBJECT) -lm -o:g' \
-e 's:$(FFLAGS) -o:$(FFLAGS) $(LDFLAGS) -o:g' \
-e '/make.system/d' \
-i *akefile || die
emake \
CC=$(tc-getCXX) \
CCFLAGS="${CXXFLAGS}"
if [[ -f pNNMAKE. ]]; then
mv pNNMAKE{.,} || die
emake almostsuperclean
else
emake clean
fi
}
for i in src/{mfr2rosetta,SPARTA/src,pdbrms,TALOS,rosettaFrag2csFrag,nnmake}; do
pushd ${i} > /dev/null
compilation
popd > /dev/null
done
}
src_install() {
insinto /opt/${PN}/
doins -r *
chmod 755 \
"${ED}"/opt/${PN}/com/* \
"${ED}"/opt/${PN}/src/{mfr2rosetta/mfr2rosetta,SPARTA/src/SPARTA,pdbrms/pdbrms,TALOS/TALOS,rosettaFrag2csFrag/rosettaFrag2csFrag,nnmake/pNNMAKE} \
|| die
dosym make_fragments_2000.pl /opt/${PN}/com/make_fragment_2000.pl
doenvd "${T}"/39${PN}
}
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