Merge pull request #33 from mariux64/rebuild-python-2.7.15-1-to-2

Rebuild python 2.7.15 1 to 2

python-2.7.15-2.build.sh

@@ -0,0 +1,277 @@
+#! /bin/bash
+
+PKG=python
+VERSION=2.7.15
+BUILD=2
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+# PREFIX=/dev/shm/pkg/$PKG-$VERSION-$BUILD
+
+XPYTHONVER=2.7
+XPYTHONLIB=$PREFIX/lib/python$XPYTHONVER/site-packages
+
+PATH=/bin:/usr/bin:/usr/sbin:/usr/local/package/bin:/usr/local/bin
+export PATH
+
+set -xe
+umask 022
+
+BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp
+test -d $BUILD_TMPDIR && 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
+EOF
+. $PREFIX/profile
+
+export MAKEFLAGS="-j $(nproc)"
+
+BUILDDIR=$PREFIX/build
+
+mkdir -p $BUILDDIR
+cd $BUILDDIR
+
+function plaininstall() {
+	local dir=$1
+	local tar=$2
+	local url=$3
+	(
+		cd $BUILDDIR
+		test -e $tar || wget $url
+		test -d $dir || tar xvf $tar
+		cd $dir
+		./configure --prefix=$PREFIX
+		make -j $(nproc)
+		make install
+	)
+}
+
+URL=https://www.python.org/ftp/python/$VERSION/Python-$VERSION.tgz
+test -e Python-$VERSION.tgz || wget $URL
+test -d Python-$VERSION || tar xf Python-$VERSION.tgz
+cd Python-$VERSION
+
+# Required for "Thenao" , bad for virtualenv --enable-shared
+# Required for tensorflow : --enable-unicode=ucs4;
+./configure --prefix=$PREFIX --enable-shared LDFLAGS=-Wl,-rpath,$PREFIX/lib --enable-unicode=ucs4
+make
+make install
+
+cd $PREFIX
+python -m ensurepip
+pip install --upgrade pip
+
+pip install distribute	# requested by sven klages. For unknown reasons must be installed early
+
+pip install Pillow
+pip install virtualenv
+
+pip install NumPy Matplotlib pandas SymPy nose
+
+pip install ipython[all]
+pip install ipywidgets
+pip install scikit-learn
+pip install seaborn
+
+pip install bx-python # now at version 0.8.1
+
+pip install Cython	# for metaseq,pygpu
+pip install pycurl	# for metaseq
+pip install metaseq
+
+pip install macs2
+pip install HTSeq
+
+# for sasse: Theano and tensorflow (cuda version)
+
+# install libgpuarray/pygpu for Tensorflow
+(
+	VER=0.7.6
+	cd build
+	test -e libgpuarray-$VER.tar.gz || wget -O libgpuarray-$VER.tar.gz https://codeload.github.com/Theano/libgpuarray/tar.gz/v$VER
+	test -d libgpuarray-$VER || tar xf libgpuarray-$VER.tar.gz
+	cd libgpuarray-$VER
+	test -d Build || mkdir Build
+	cmake -DCMAKE_INSTALL_PREFIX=$PREFIX .
+	make
+	make install
+	python setup.py build_ext -L $PREFIX/lib -I $PREFIX/include
+	python setup.py install
+)
+
+pip install Theano
+
+# these dickheads like to downgrade numpy, because there where problems on windows!
+# https://github.com/tensorflow/tensorflow > 88917888f509e3e61ffe632534476e7b09d3326a
+echo 'numpy >= 1.15.1' > $BUILDDIR/dont_clobber_numpy_on_linux
+pip install tensorflow-gpu --constraint $BUILDDIR/dont_clobber_numpy_on_linux
+
+pip install biopython	# wird von bressin fuer python3 benutzt. klingt gut, ist in metaseq requirement drin
+pip install git+git://github.com/tanghaibao/jcvi.git # angefragt von Dr. Jun Yang
+
+# for Klages
+#
+# we need cairo otherwise pygtk won't do the gtk stuff and pygtk.h
+# if we install cairo with wheel, we dont get a pkg-config file.
+pip install --no-binary :all: pycairo
+pip install GPy distribute h5py igraph ranger pep8
+plaininstall pygobject-2.28.7 pygobject-2.28.7.tar.xz https://ftp.gnome.org/pub/gnome/sources/pygobject/2.28/pygobject-2.28.7.tar.xz
+plaininstall pygtk-2.24.0 pygtk-2.24.0.tar.gz https://ftp.gnome.org/pub/GNOME/sources/pygtk/2.24/pygtk-2.24.0.tar.gz
+# no new packages since apr 2010
+plaininstall pygtksourceview-2.10.1 pygtksourceview-2.10.1.tar.gz https://ftp.gnome.org/pub/gnome/sources/pygtksourceview/2.10/pygtksourceview-2.10.1.tar.gz
+plaininstall dbus-python-1.2.8 dbus-python-1.2.8.tar.gz https://dbus.freedesktop.org/releases/dbus-python/dbus-python-1.2.8.tar.gz
+
+(
+	cd build
+	# nothing new since Apr 2011
+	test -e py2cairo-1.10.0.tar.gz || wget https://www.cairographics.org/releases/py2cairo-1.10.0.tar.bz2
+	test -d py2cairo-1.10.0 || tar xf py2cairo-1.10.0.tar.bz2
+	cd py2cairo-1.10.0
+	./waf configure --prefix=$PREFIX
+	./waf build
+	./waf install
+)
+
+pip install keras
+pip install deeptools   # Alena vom Boemmel -> helpdesk 19.04.2017, 3.0.1 Laura Glaser -> Helpdesk 05.03.2018
+
+pip install sphinx
+pip install recommonmark # Sabrina Krakau -> Helpdesk 21.06.2017
+pip install fastcluster # Peter Arndt -> Helpdesk: PANNZER - dependencies, 21.07.2017
+
+pip install umi_tools # Sven Klages -> Helpdesk 11.09.2017
+
+# bunch of packages # Thomas Risch -> Helpdesk 20.11.2017 Topic: 'Cellprofiler', wxPython and gdal left out
+# (11 plus deps)    # wxPython might cause trouble with existing wxWidgets, gdal build needs more investigation
+pip install pytest
+pip install cellh5
+pip install centrosome
+pip install prokaryote
+pip install inflect
+pip install javabridge
+pip install libtiff
+pip install pydot
+pip install pygraphviz
+pip install python-bioformats
+pip install MySQL-python
+
+pip install CrossMap # Laura Glaser -> Helpdesk 07.12.2017
+
+pip install cutadapt   # Sabrina Krakau,  23.01.2018 (phd Seminar)
+
+# to be removed from system. Install here:
+
+plaininstall libxml2-2.9.8 libxml2-2.9.8.tar.gz http://xmlsoft.org/sources/libxml2-2.9.8.tar.gz
+# nothing new since Mar 2012
+plaininstall gnome-doc-utils-0.20.10 gnome-doc-utils-0.20.10.tar.xz https://ftp.gnome.org/pub/gnome/sources/gnome-doc-utils/0.20/gnome-doc-utils-0.20.10.tar.xz
+pip install pssh
+
+(
+	cd $BUILDDIR
+	test -e iotop-0.6.tar.gz || wget http://guichaz.free.fr/iotop/files/iotop-0.6.tar.gz
+	test -d iotop-0.6 || tar xf iotop-0.6.tar.gz
+	cd iotop-0.6
+	python setup.py install
+	mv $PREFIX/sbin/iotop $PREFIX/bin
+	rmdir $PREFIX/sbin
+)
+
+# win remote tools, linux alternativen zur power-shell, kreitler 06.03.2018
+pip install pywinrm
+pip install ptwinrm
+pip install winremote
+
+pip install joblib    # helpdesk mail (03/28/18 13:22, Denise Thiel)
+
+pip install MotifScan # Alena 30.8.2018
+pip install MAmotif
+
+pip install hic2cool  # helpdesk robert schoepflin 17.09.2018
+pip install hifive
+
+# https://hicexplorer.readthedocs.io/en/latest/index.html
+# HiCExplorer likes to downgrade practically everyting ...
+cat <<__CONSTRAINTS > $BUILDDIR/such_a_lamer
+numpy >= 1.13
+scipy >= 1.0
+matplotlib >= 2.1
+pysam >= 0.11
+intervaltree >= 2.1
+biopython >= 1.68
+tables >= 3.3
+pandas >= 0.20
+pyBigWig >= 0.3
+six >= 1.10
+future >= 0.16
+cooler >= 0.7
+jinja2 >= 2.9
+unidecode >= 0.4
+configparser >= 3.5
+__CONSTRAINTS
+
+# setup.py bdist_wheel for HiCExplorer fails, but setup.py install
+# creates a working executable, so don't get confused.
+pip install HiCExplorer --constraint $BUILDDIR/such_a_lamer --no-warn-conflicts
+
+(
+	SIP_VERSION=4.19.13
+	SIP_SRC=https://sourceforge.net/projects/pyqt/files/sip/sip-$SIP_VERSION/sip-$SIP_VERSION.tar.gz
+
+	cd $BUILDDIR
+	test -e sip-$SIP_VERSION.tar.gz || wget $SIP_SRC
+	test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz
+
+	cd sip-$SIP_VERSION
+
+	python configure.py\
+	    -b $PREFIX/bin \
+	    -d $XPYTHONLIB \
+	    -e $PREFIX/include/python$XPYTHONVER \
+	    -v $PREFIX/share/sip
+
+	mkdir -p $PREFIX/share/sip
+	make; make install
+)
+
+(
+	# Don't use 5.11.3 !
+	PYQT_VERSION=5.10.1
+	PYQT_SRC=https://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-$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
+
+	python configure.py \
+	  -b $PREFIX/bin \
+	  -d $XPYTHONLIB \
+	  -q /usr/local/qt5/bin/qmake \
+	  -v $PREFIX/share/sip \
+	  --confirm-license \
+	  --no-designer-plugin \
+	  --no-python-dbus \
+	  --no-qml-plugin \
+	  --no-stubs \
+	  --sip-incdir=$PREFIX/include/python$XPYTHONVER \
+	  --verbose
+
+	make -j $(nproc); make install
+)
+
+cp -pr $PREFIX/man $PREFIX/share
+rm -r $PREFIX/man
+
+# exit 1 # final test, inhibits 'closing' on success
+exit