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executable file 224 lines (179 sloc) 6.86 KB
#! /bin/bash
PKG=python
VERSION=3.7.4
BUILD=2
PYTHONVER=${VERSION%.*}
PREFIX=/pkg/$PKG-$VERSION-$BUILD
if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
set -xe
umask 022
BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp
test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR )
mkdir -p $BUILD_TMPDIR/home
export TMPDIR=$BUILD_TMPDIR
export HOME=$BUILD_TMPDIR/home
exec </dev/null
mkdir -p $PREFIX
cat >$PREFIX/profile <<-EOF
PATH=$PREFIX/bin:\$PATH
PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH}
export PKG_CONFIG_PATH
if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi
EOF
. $PREFIX/profile
export MAKEFLAGS="-j $(nproc)"
BUILDDIR=$PREFIX/build
mkdir -p $BUILDDIR
cd $BUILDDIR
test -e Python-$VERSION.tar.xz || wget https://www.python.org/ftp/python/$VERSION/Python-$VERSION.tar.xz
test -d Python-$VERSION || tar xvf Python-$VERSION.tar.xz
cd Python-$VERSION
LDFLAGS="-Wl,-rpath=$PREFIX/lib" \
./configure \
--prefix=$PREFIX \
--enable-shared
make -j $(nproc)
# make test || true # 'test_socket' seems to run for ever
make install
( # sip: tool to create Python bindings for C and C++ libraries.
cd $PREFIX/build
SIP_VERSION=4.19.18
SIP_SRC=https://www.riverbankcomputing.com/static/Downloads/sip/$SIP_VERSION/sip-$SIP_VERSION.tar.gz
test -e sip-$SIP_VERSION.tar.gz || wget $SIP_SRC
test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz
cd sip-$SIP_VERSION
python3 configure.py \
-b $PREFIX/bin \
-d $PREFIX/lib/python$PYTHONVER/site-packages \
-e $PREFIX/include/python${PYTHONVER}m \
-v $PREFIX/share/sip \
--sip-module=sip
# well, right here share/sip is spoilage, but maybe some packages will use the decent sip later on ...
mkdir -p $PREFIX/share/sip
make -j $(nproc);
make install
)
( # now for the private (sic!) version required by newer PyQt
cd $PREFIX/build
mkdir -p private_sip
cd private_sip
SIP_VERSION=4.19.18
SIP_SRC=https://www.riverbankcomputing.com/static/Downloads/sip/$SIP_VERSION/sip-$SIP_VERSION.tar.gz
test -e sip-$SIP_VERSION.tar.gz || wget $SIP_SRC
test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz
cd sip-$SIP_VERSION
# note $PREFIX/share/sip/PyQt5 is mandatory
python3 configure.py \
-d $PREFIX/lib/python$PYTHONVER/site-packages \
-v $PREFIX/share/sip/PyQt5 \
--no-tools \
--sip-module=PyQt5.sip
mkdir -p $PREFIX/share/sip/PyQt5
make -j $(nproc)
# The resulting sip.so in site-packages/PyQt5 differs indeed a bit (grep for PyQt5)
make install
)
(
PYQT_VERSION=5.13.0
PYQT_SRC=https://www.riverbankcomputing.com/static/Downloads/PyQt5/$PYQT_VERSION/PyQt5_gpl-$PYQT_VERSION.tar.gz
cd $BUILDDIR
test -e PyQt5_gpl-$PYQT_VERSION.tar.gz || wget $PYQT_SRC
test -d PyQt5_gpl-$PYQT_VERSION || tar -xf PyQt5_gpl-$PYQT_VERSION.tar.gz
cd PyQt5_gpl-$PYQT_VERSION
# export QTDIR=/usr/local/qt5
python3 configure.py \
-b $PREFIX/bin \
-d $PREFIX/lib/python$PYTHONVER/site-packages \
-n $PREFIX/share/qsci \
-q /usr/local/qt5/bin/qmake \
-v $PREFIX/share/sip/PyQt5 \
--sip-incdir=$PREFIX/include/python${PYTHONVER}m \
--confirm-license \
--no-qml-plugin \
--no-designer-plugin \
--no-dist-info \
--verbose
make -j $(nproc)
# Did I miss something in the docs ???
# w/o the *.so files inplace a clean 'make install' fails with file not found ...
# -> FileNotFoundError: [Errno 2] No such file or directory:
# '/dev/shm/python-3.7.4-0/lib/python3.7/site-packages/PyQt5/QtCore.so'
mkdir -p $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
for F in `find | grep '\.so$' | grep -v '/lib'` ; do
cp -vp $F $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5/
done
make install
)
(
QSCINTILLA_VERSION=2.11.2
QSCINTILLA_SRC=https://www.riverbankcomputing.com/static/Downloads/QScintilla/$QSCINTILLA_VERSION/QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz
cd $BUILDDIR
test -e QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz || wget $QSCINTILLA_SRC
test -d QScintilla_gpl-$QSCINTILLA_VERSION || tar -xf QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz
cd QScintilla_gpl-$QSCINTILLA_VERSION
cd Python
# apidir follows PyQt, not Qt (default is: QT_INSTALL_DATA/qsci)
# creation of PEP 376 .dist-info fails in $PREFIX/share
python3 configure.py \
--pyqt=PyQt5 \
--qmake=/usr/local/qt5/bin/qmake \
--apidir=$PREFIX/share/qsci \
--no-dist-info
make -j $(nproc)
# Call it a deja-vu, nerve ...
# -> FileNotFoundError: [Errno 2] No such file or directory: '/dev/shm/python-3.7.4-0/lib/python3.7/site-packages/PyQt5/Qsci.so'
mkdir -p $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
for F in `find | grep '\.so$' | grep -v '/lib'` ; do
cp -vp $F $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
done
make install
)
python3 -m ensurepip
pip3 install -I pip
pip3 install ipython[all]
pip3 install SciPy NumPy Matplotlib pandas SymPy nose statsmodels
# clean up some dirt that statsmodels placed also into $PREFIX
rm -vf $PREFIX/LICENSE.txt
rm -vf $PREFIX/setup.cfg
pip3 install Cython
pip3 install pysam
pip3 install seaborn
pip3 install scikit-learn
# pip3 install metaseq # fails (Latest commit fa875d1 on Jan 10, 2017)
pip3 install Mako
pip3 install meson # required in mariux
pip3 install cutadapt # Helpdesk 01/24/18 16:19, Sabrina Krakau
pip3 install pygobject # Helpdesk 03/26/18 14:19, Virginie Stanisla
pip3 install blink1 # Blink1-lib 07/04/18 12:00, Niclas Hofmann
pip3 install umi-tools
pip3 install sphinx
pip3 install recommonmark
pip3 install fastcluster
pip3 install pydot
pip3 install pygraphviz
pip3 install deeptools
pip3 install HTSeq
pip3 install keras
pip3 install MotifScan # Alena 30.8.2018
pip3 install MAmotif
pip3 install hic2cool # Helpdesk Robert Schoepflin 17.09.2018
# pip3 install hifive # only python 2.7+
pip3 install snakemake
pip3 install virtualenv # Donald
pip3 install odfpy # Donald
pip3 install Dumper # Thomas
pip3 install igraph
pip3 install louvain # monocle3 prep for Helene
pip3 install selenium # 19.7.19 Kreitler -> https://webxray.org/
pip3 install cooltools # Maria Valieva 17.7.2019
pip3 install gmpy # From viper context (Helpdesk Laura Glaser 9.8.2019)
# pip3 install HiCExplorer # Would be a nice to have, but it likes to downgrade too much, pick some cherries
pip3 install HiCMatrix
pip3 install pyGenomeTracks
pip3 install python-bioformats
pip3 install jupyterlab # request Peter Arndt
pip3 install libxml2-python3 # required by several bee packages after swich to python3
pip3 install scour # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98
pip3 install jupyterlab-git # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/96
exit