python 2.7.15: Rebuild with some new packages

Most prominent change is the usage of version constraints with pip.
This avoids that some debrained package degrades existing ones
without need (thus we are able to keep a recent numpy 1.15.1).

python-2.7.15-1.build.sh

@@ -0,0 +1,218 @@
+#! /bin/bash
+
+PKG=python
+VERSION=2.7.15
+BUILD=1
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+# PREFIX=/dev/shm/pkg/$PKG-$VERSION-$BUILD
+
+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
+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 $PREFIX/include
+	python setup.py install
+)
+
+pip install Theano
+
+# these dickheads like to downgrade numpy, because there where problems on windows!
+# https://github.com/tensorflow/tensorflow > 88917888f509e3e61ffe632534476e7b09d3326a
+echo 'numpy >= 1.15.1' > dont_clobber_numpy_on_linux
+pip install tensorflow-gpu --constraint dont_clobber_numpy_on_linux
+
+pip install biopython	# wird von bressin fuer python3 benutzt. klingt gut, ist in metaseq requirement drin
+pip install git+git://github.com/tanghaibao/jcvi.git # angefragt von Dr. Jun Yang
+
+# for Klages
+#
+# we need cairo otherwise pygtk won't do the gtk stuff and pygtk.h
+# if we install cairo with wheel, we dont get a pkg-config file.
+pip install --no-binary :all: pycairo
+pip install GPy distribute h5py igraph ranger pep8
+plaininstall pygobject-2.28.7 pygobject-2.28.7.tar.xz https://ftp.gnome.org/pub/gnome/sources/pygobject/2.28/pygobject-2.28.7.tar.xz
+plaininstall pygtk-2.24.0 pygtk-2.24.0.tar.gz https://ftp.gnome.org/pub/GNOME/sources/pygtk/2.24/pygtk-2.24.0.tar.gz
+# no new packages since apr 2010
+plaininstall pygtksourceview-2.10.1 pygtksourceview-2.10.1.tar.gz https://ftp.gnome.org/pub/gnome/sources/pygtksourceview/2.10/pygtksourceview-2.10.1.tar.gz
+plaininstall dbus-python-1.2.8 dbus-python-1.2.8.tar.gz https://dbus.freedesktop.org/releases/dbus-python/dbus-python-1.2.8.tar.gz
+
+(
+	cd build
+	# nothing new since Apr 2011
+	test -e py2cairo-1.10.0.tar.gz || wget https://www.cairographics.org/releases/py2cairo-1.10.0.tar.bz2
+	test -d py2cairo-1.10.0 || tar xf py2cairo-1.10.0.tar.bz2
+	cd py2cairo-1.10.0
+	./waf configure --prefix=$PREFIX
+	./waf build
+	./waf install
+)
+
+pip install keras
+pip install deeptools   # Alene 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 > 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
+
+pip install HiCExplorer --constraint such_a_lamer --no-warn-conflicts
+
+# exit 1 # final test, inhibits 'closing' on success
+exit