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# Maintainer: Michael Schubert <mschu.dev at gmail>
# Maintainer: Eugene Dvoretsky <radioxoma at gmail>
pkgname=cellprofiler-git
pkgver=2.2.0.PR.1.r1148.gd30878ec3
pkgrel=1
pkgdesc="Analysis software for cellular images"
arch=('i686' 'x86_64')
url="http://www.cellprofiler.org/"
license=('GPL')
depends=(
'python2-appdirs'
'python2-decorator'
'python2-pytz'
'python2-pyzmq'
'python2-numpy'
'python2-scipy'
'python2-matplotlib'
'python2-h5py'
'python2-imaging'
'python2-scikit-image'
'python2-pylibtiff-git'
'python2-pandas'
'python2-raven'
'python2-lxml'
'mysql-python'
'wxpython'
# 'pythoh2-cellh5'
'python2-hmmlearn-git'
'python2-pywavelets'
'python2-mahotas'
'python2-joblib'
'python2-javabridge'
'python2-bioformats'
'python2-prokaryote'
'python2-centrosome')
makedepends=('python2-pip' 'cython2' 'python2-pytest')
optdepends=(
'cellprofiler-analyst: analyze imaging datasets'
'ilastik: interactive segmentation')
provides=('cellprofiler')
source=("cellprofiler::git+https://github.com/CellProfiler/CellProfiler.git#commit=d30878ec372485b6c7c222ea0cb7ccb23590a820"
"cellprofiler.desktop")
# Note: impossible to run tag=2.2.0 on current Archlinux 2017-05-04 due to matplotlib API changes https://github.com/CellProfiler/CellProfiler/issues/2581
sha256sums=('SKIP'
'039350ce852b1efb8e9e11db94ca0ab01a34f32cc5aaf2acf524e19e2fa04d6f')
pkgver() {
cd cellprofiler
git describe --long --tags | sed 's/\([^-]*-g\)/r\1/;s/-/./g'
}
build() {
cd "$srcdir/cellprofiler"
export PYTHONPATH="${srcdir}/pkg/lib/python2.7/site-packages"
# Non-AUR or official repo dependencies will be fetched into $srcdir directory by pip
# No write permission to $pkgdir in `build()` funtion, so we are using `$srcdir/pkg` for pip
# MUST be run on machine without installed CellProfiler or dependencides won't be fetched
PIP_CONFIG_FILE=/dev/null pip2 install --prefix="$srcdir/pkg" .
}
package() {
cd "$srcdir/cellprofiler"
install -Dm644 LICENSE "$pkgdir/usr/share/licenses/cellprofiler/LICENSE"
install -Dm644 artwork/CellProfilerIcon.png "$pkgdir/usr/share/pixmaps/cellprofiler.png"
install -Dm644 "$srcdir/cellprofiler.desktop" "$pkgdir/usr/share/applications/cellprofiler.desktop"
cp -r "$srcdir/pkg/." "$pkgdir/usr"
echo '3.0.0rc1' > "$pkgdir/usr/lib/python2.7/site-packages/cellprofiler/VERSION"
}
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