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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit java-pkg-2 java-pkg-simple prefix python-r1 versionator
MY_PV="$(delete_all_version_separators $(get_version_component_range 1-2))"
MY_PATCH="20120106"
MY_P="${PN}-v${MY_PV}-linux"
DESCRIPTION="Predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins"
HOMEPAGE="http://shiftx2.wishartlab.com/"
SRC_URI="http://shiftx2.wishartlab.com/download/${MY_P}-${MY_PATCH}.tgz"
SLOT="0"
LICENSE="all-rights-reserved"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="debug"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
CDEPEND="dev-util/weka ${PYTHON_DEPS}"
RDEPEND="${CDEPEND}
${PYTHON_DEPS}
dev-lang/R
sci-biology/ncbi-tools
sci-chemistry/reduce
>=virtual/jre-1.5"
DEPEND="${CDEPEND}
>=virtual/jdk-1.5"
S="${WORKDIR}"/${MY_P}
QA_PREBUILT="/opt/.*"
src_prepare() {
epatch \
"${FILESDIR}"/${P}-java.patch \
"${FILESDIR}"/${P}-system.patch
rm "${S}"/src/FeatureRanges.java || die
shared=$(echo "${EPREFIX}/usr/share/${PN}" | sed -e 's/\//\\\//g')
sed -i -e "s/PUT_GENTOO_SHARE_PATH_HERE/${shared}/g" "${S}/src/ShiftXp.java" || die
if use debug; then
sed -i -e 's/DEBUG = false/DEBUG = true/g' "${S}/src/ShiftXp.java" || die
fi
# hack alert!
sed \
-e '/-o/s:$(GCC):$(GCC) $(LDFLAGS):g' \
-e '/-o/s:$(CC):$(CC) $(LDFLAGS):g' \
-i modules/*/Makefile || die
sed -e '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die
eprefixify ${PN}.py
}
src_compile() {
mkdir "${S}"/build || die
ejavac -classpath "$(java-pkg_getjars weka)" -nowarn \
-d "${S}"/build $(find src/ -name "*.java")
jar cf "${PN}.jar" -C "${S}"/build . || die
einfo "Building module angles"
cd "${S}"/modules/angles || die
emake clean
emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" get_angles phipsi
einfo "Building module resmf"
cd "${S}"/modules/resmf || die
emake clean
emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" resmf
einfo "Building module effects"
cd "${S}"/modules/effects || die
emake clean
emake CFLAGS="${CFLAGS}" CC=$(tc-getCC) LINK="${LDFLAGS}" all
}
src_install() {
java-pkg_dojar "${PN}.jar"
java-pkg_dolauncher j${PN} --main "ShiftXp" --pkg_args "-dir ${EPREFIX}/usr/bin"
insinto /usr/share/${PN}
doins "${S}"/lib/{limitedcshift.dat,RandomCoil.csv,data-header.arff}
doins -r "${S}"/lib/predmodels
insinto /usr/share/${PN}/vader
doins -r "${S}"/modules/resmf/lib/*
local instdir="/opt/${PN}"
dodoc README 1UBQ.pdb
python_foreach_impl python_newscript ${PN}.py ${PN}
mv shiftx2_util.py shiftx2util.py || die
python_moduleinto ${PN}
touch __init__.py
python_foreach_impl python_domodule natsorted.py shiftx2util.py __init__.py
# other modules
dobin \
"${S}"/modules/angles/{get_angles,phipsi} \
"${S}"/modules/resmf/resmf \
"${S}"/modules/effects/caleffect
# script
python_foreach_impl python_doscript "${S}"/script/*py
exeinto ${instdir}/script
doexe "${S}"/script/*.r
# shifty3
python_foreach_impl python_newscript "${S}"/shifty3/*py shifty3
exeinto ${instdir}/shifty3
doexe "${S}"/shifty3/xalign_x
dosym ../${PN}/shifty3/xalign_x /opt/bin/xalign_x
insinto ${instdir}/shifty3
doins -r "${S}"/shifty3/{blastdb,refdb,xalign.parms,wt.rbo}
python_foreach_impl python_doscript "${S}"/shifty3/utils/*py
dobin "${S}"/shifty3/utils/create_blastdb.sh
}
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