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# Contributr Joshua Hardy <joshinsilico@gmail.com>
pkgname='scipion-git'
pkgver=v1.0.1.r12.1dfd3db7fa
pkgrel=1
pkgdesc="An integrative software platform used to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)"
arch=('x86_64')
url="https://github.com/I2PC/scipion"
license=('GPL')
depends=(
'cmake'
'fftw'
'freeglut'
'gawk'
'gcc'
'gnuplot'
'gsl'
'jdk8-openjdk'
'lapack'
'lib32-gcc-libs'
'libjpeg6-turbo'
'libxft'
'libxml++'
'libxslt'
'make'
'openjpeg2'
'openmpi'
'python2'
'tk'
)
makedepends=('git')
provides=("${pkgname%-git}")
conflicts=("${pkgname%-git}")
optdepends=(
'ctffind3-ctftilt'
'ctffind4'
'eman2'
# 'gctf'
'motioncor2'
'relion'
# 'resmap'
'simple2'
'spiderweb'
'summovie'
# 'ucsf-chimera'
'unblur'
)
options=('!strip')
source=(
'git+https://github.com/I2PC/scipion.git'
'scipion.csh'
'scipion.sh'
)
md5sums=(
'SKIP'
'SKIP'
'SKIP'
)
pkgver() {
cd "$srcdir/scipion"
printf "%s" "$(git describe --long | sed 's/\([^-]*-\)g/r\1/;s/-/./g')"
}
build() {
cd "$srcdir/scipion"
_NPROC=$(nproc --all)
sed -i -e s:"MPI_LIBDIR = /usr/lib64/mpi/gcc/openmpi/lib":"MPI_LIBDIR = /usr/lib/openmpi":g config/templates/scipion.template
sed -i -e s:"MPI_INCLUDE = /usr/lib64/mpi/gcc/openmpi/include":"MPI_INCLUDE = /usr/include":g config/templates/scipion.template
sed -i -e s:"MPI_BINDIR = /usr/lib64/mpi/gcc/openmpi/bin":"MPI_BINDIR = /usr/bin":g config/templates/scipion.template
sed -i -e s:"JAVA_HOME = /usr/lib/jvm/java-7-openjdk":"JAVA_HOME = /usr/lib/jvm/default":g config/templates/scipion.template
./scipion config --overwrite
./scipion install -j $_NPROC --no-opencv --no-scipy
# ln -s /opt/ucsf-chimera software/em/chimera
mkdir software/em/ctffind4
ln -s /usr/bin/ctffind software/em/ctffind4/ctffind
ln -s /opt/eman2 software/em/eman2.12
ln -s /opt/relion software/em/relion-1.4
# ln -s /opt/resmap software/em/resmap
ln -s /opt/simple2 software/em/simple
ln -s /opt/spider software/em/spider
mkdir -p software/em/summovie/bin
ln -s /usr/bin/summovie software/em/summovie/bin/sum_movie_openmp_7_17_15.exe
mkdir software/em/unblur
ln -s /usr/bin/unblur* software/em/.
}
package() {
cd "${srcdir}"/scipion
install -d "${pkgdir}"/opt "${pkgdir}"/etc/profile.d
cp -r "${srcdir}"/scipion "${pkgdir}"/opt/.
install -D -m755 "${srcdir}"/scipion.sh "${pkgdir}"/etc/profile.d/.
install -D -m755 "${srcdir}"/scipion.csh "${pkgdir}"/etc/profile.d/.
}
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