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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
# Versioning is output of nmrPipe -help
EAPI=8
inherit virtualx
DESCRIPTION="Spectral visualisation, analysis and Fourier processing"
HOMEPAGE="https://www.ibbr.umd.edu/nmrpipe"
#SRC_URI="
# NMRPipeX.tZ
# talos.tZ
# dyn.tZ
# binval.com
# install.com"
SRC_URI="
https://www.ibbr.umd.edu/nmrpipe/install.com -> install-${PV}.com
https://www.ibbr.umd.edu/nmrpipe/binval.com -> binval-${PV}.com
https://www.ibbr.umd.edu/nmrpipe/NMRPipeX.tZ -> NMRPipeX-${PV}.tZ
https://www.ibbr.umd.edu/nmrpipe/plugin.smile.tZ -> plugin.smile-${PV}.tZ
https://www.ibbr.umd.edu/nmrpipe/talos.tZ -> talos-${PV}.tZ
https://www.ibbr.umd.edu/nmrpipe/dyn.tZ -> dyn-${PV}.tZ
"
SLOT="0"
LICENSE="nmrpipe"
# Right now, precompiled executables are only available for Linux on the
# x86 architecture. The maintainer chose to keep the sources closed, but
# says he will gladly provide precompiled executables for other platforms
# if there are such requests.
KEYWORDS="~amd64 ~x86"
RESTRICT="strip bindist mirror !test? ( test )"
DEPEND="app-shells/tcsh"
RDEPEND="${DEPEND}
app-editors/nedit
dev-lang/tk
dev-tcltk/blt
media-fonts/font-sun-misc
sys-libs/ncurses-compat:5/5
x11-apps/xset
x11-libs/xview-bin
!prefix? ( >=x11-libs/libX11-1.6.2 )
prefix? ( dev-util/patchelf )"
S="${WORKDIR}/NMR"
NMRBASE="/opt/${PN}"
ENMRBASE="${EPREFIX}/${NMRBASE}"
QA_PREBUILT="opt/.*"
src_unpack() {
# The installation script will unpack the package. We just provide symlinks
# to the archive files, ...
for i in NMRPipeX-${PV}.tZ plugin.smile-${PV}.tZ talos-${PV}.tZ dyn-${PV}.tZ; do
ln -sf "${DISTDIR}"/${i} ${i/-${PV}/} || die
done
mkdir "${S}" && cd "${S}" || die
# ... copy the installation scripts ...
cp -L "${DISTDIR}"/install-${PV}.com install.com || die
cp -L "${DISTDIR}"/binval-${PV}.com binval.com || die
# ... and make the installation scripts executable.
chmod +x *.com || die
VIRTUALX_COMMAND="csh"
virtx \
./install.com \
+type $(usex x86 linux9 linux212_64) \
+src "${WORKDIR}" \
+dest "${S}" \
+nopost +nocshrc
}
src_prepare() {
default
local bin i
mv nmrbin.$(usex x86 linux9 linux212_64)/nmr{W,w}ish || die
ebegin "Cleaning installation"
# Remove some of the bundled applications and libraries; they are provided by Gentoo instead.
rm -rf nmrbin.linux*/{lib/*.timestamp,*timestamp,xv,gnuplot*,rasmol*,nc,nedit} \
nmrbin.{linux,mac} nmruser format \
$(usex x86 nmrbin.linux212_64 nmrbin.linux9) \
|| die "Failed to remove unnecessary libraries."
# As long as xview is not fixed for amd64 we do this
rm nmrbin.linux*/lib/{libxview.so*,libolgx.so*} || die
# Remove the initialisation script generated during the installation.
# It contains incorrect hardcoded paths; only the "nmrInit.com" script
# should be used.
rm -f com/nmrInit.linux*.com || die "Failed to remove broken init script."
# Remove installation log files.
rm -f README_NMRPIPE_USERS *.log install.com binval.com || die "Failed to remove installation log."
# Remove unused binaries
rm -f {talos*,spartaplus,promega}/bin/*{linux,mac,sgi6x,winxp} pdb/misc/addSeg || die
# Some scripts are on the wrong place
cp -f nmrtxt/*.com com/
rm -f {acme,com}/{nmrproc,fid,install}.com || die
eend
ebegin "Fixing paths in scripts"
# Set the correct path to NMRPipe in the auxiliary scripts.
for i in $(find com/ dynamo/surface/misc/ nmrtxt/ talos/misc talosplus/com -type f); do
sed -e "s%/u/delaglio%${ENMRBASE}%" -i ${i} || die \
"Failed patching scripts."
done
sed -i "s:${WORKDIR}:${ENMRBASE}:g" com/font.com || die
sed \
-e "s:!/bin:!${EPREFIX}/bin:g" \
-e "s:!/usr/bin:!${EPREFIX}/usr/bin:g" \
-e "s:!/usr/local/bin:!${EPREFIX}/usr/bin:g" \
-e "s: /bin: ${EPREFIX}/bin:g" \
-e "s: /usr/bin: ${EPREFIX}/usr/bin:g" \
-e "s: /usr/local/bin: ${EPREFIX}/usr/bin:g" \
-i $(find "${S}" \( -name "*.tcl" -o -name "*.com" -o -name "*.ksh" \)) \
{com/,nmrtxt/*.com,nmrtxt/nt/*.com,dynamo/tcl/,talos*/com/,dynamo/tcl/}* \
nmrbin.linux*/{nmrDraw,xNotify} || die
eend
if use prefix; then
sed \
-e "s: sh : \"${EPREFIX}/bin/sh\" :g" \
-e "s: csh : \"${EPREFIX}/bin/csh\" :g" \
-e "s: bash : \"${EPREFIX}/bin/bash\" :g" \
-e "s:appTerm -e:appTerm -e \"${EPREFIX}/bin/csh\":g" \
-i com/* || die
ebegin "Setting RPATH in binaries"
for bin in $(find nmrbin.linux*/ -type f -maxdepth 1); do
patchelf --set-rpath "${EPREFIX}/usr/lib/" ${bin}
done
eend $?
fi
}
src_install() {
cat >> "${T}"/nmrWish <<- EOF
#!${EPREFIX}/bin/csh -f
setenv NMRBIN \${NMRBASE}/bin/
setenv NMRLIB \${NMRBIN}/lib
setenv AUXLIB \${NMRBIN}/openwin/lib
setenv TCLPATH \${NMRBASE}/com
setenv TCL_LIBRARY \${NMRBASE}/nmrtcl/tcl8.4
setenv TK_LIBRARY \${NMRBASE}/nmrtcl/tk8.4
setenv BLT_LIBRARY \${NMRBASE}/nmrtcl/blt2.4
setenv NMRPIPE_TCL_LIB \${NMRBASE}/nmrtcl/tcl8.4
setenv NMRPIPE_TK_LIB \${NMRBASE}/nmrtcl/tk8.4
setenv NMRPIPE_BLT_LIB \${NMRBASE}/nmrtcl/blt2.4
if (!(\$?LD_LIBRARY_PATH)) then
setenv LD_LIBRARY_PATH \${NMRLIB}:\${AUXLIB}
else
setenv LD_LIBRARY_PATH \${NMRLIB}:\${LD_LIBRARY_PATH}:\${AUXLIB}
endif
nmrwish \$*
EOF
sed \
-e "s:/opt/nmrpipe:${EPREFIX}/opt/nmrpipe:g" \
-e "s:@BINTYPE@:$(usex x86 linux9 linux212_64):g" \
"${FILESDIR}"/env-${PN} \
> "${T}"/env-${PN} || die
newenvd "${T}"/env-${PN} 40${PN}
insinto ${NMRBASE}
doins -r *
dosym nmrbin.linux* ${NMRBASE}/bin
ebegin "Fixing permissions"
chmod 775 "${ED}"/${NMRBASE}/{talos*/bin/,sparta*/bin/,nmrbin.linux*/,com/,dynamo/tcl/,nmrtxt/*.com,talos*/com/,promega/bin/}* || die
eend
exeinto ${NMRBASE}/nmrbin.$(usex x86 linux9 linux212_64)
doexe "${T}"/nmrWish
insinto ${NMRBASE}/nmrtxt
doins "${FILESDIR}"/extract.M
}
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