From 8a29fc8ab7b88dd1aa6312c4400049ec28cbe001 Mon Sep 17 00:00:00 2001 From: thomas Date: Mon, 14 May 2018 15:37:24 +0200 Subject: [PATCH] python-2.7.15-0: Various package updates Manual version bumps: - bx-python 0.7.2 -> 0.8.1 - libgpuarray 0.7.5 -> 0.7.6 - dbus-python 1.1.1 -> 1.2.8 - libxml2 2.9.4 -> 2.9.8 New packages: - joblib --- python-2.7.15-0.build.sh | 186 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 186 insertions(+) create mode 100755 python-2.7.15-0.build.sh diff --git a/python-2.7.15-0.build.sh b/python-2.7.15-0.build.sh new file mode 100755 index 0000000..b8a8150 --- /dev/null +++ b/python-2.7.15-0.build.sh @@ -0,0 +1,186 @@ +#! /bin/bash + +PKG=python +VERSION=2.7.15 +BUILD=0 + +PREFIX=/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 $PREFIX/profile <<-EOF + PATH=$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 $PREFIX/include + python setup.py install +) + +pip install Theano +pip install tensorflow-gpu + +pip install biopython # wird von bressin fuer python3 benutzt. klingt gut, ist in metaseq requirement drin +pip install git+git://github.com/tanghaibao/jcvi.git # angefragt von Dr. Jun Yang + +# for Klages +# +# we need cairo otherwise pygtk won't do the gtk stuff and pygtk.h +# if we install cairo with wheel, we dont get a pkg-config file. +pip install --no-binary :all: pycairo +pip install GPy distribute h5py igraph ranger pep8 +plaininstall pygobject-2.28.7 pygobject-2.28.7.tar.xz https://ftp.gnome.org/pub/gnome/sources/pygobject/2.28/pygobject-2.28.7.tar.xz +plaininstall pygtk-2.24.0 pygtk-2.24.0.tar.gz https://ftp.gnome.org/pub/GNOME/sources/pygtk/2.24/pygtk-2.24.0.tar.gz +# no new packages since apr 2010 +plaininstall pygtksourceview-2.10.1 pygtksourceview-2.10.1.tar.gz https://ftp.gnome.org/pub/gnome/sources/pygtksourceview/2.10/pygtksourceview-2.10.1.tar.gz +plaininstall dbus-python-1.2.8 dbus-python-1.2.8.tar.gz https://dbus.freedesktop.org/releases/dbus-python/dbus-python-1.2.8.tar.gz + +( + cd build + # nothing new since Apr 2011 + test -e py2cairo-1.10.0.tar.gz || wget https://www.cairographics.org/releases/py2cairo-1.10.0.tar.bz2 + test -d py2cairo-1.10.0 || tar xf py2cairo-1.10.0.tar.bz2 + cd py2cairo-1.10.0 + ./waf configure --prefix=$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) + + +# exit 1 # final test, inhibits 'closing' on success +exit