diff --git a/python-2.7.14-1.build.sh b/python-2.7.14-1.build.sh new file mode 100755 index 0000000..9cb7901 --- /dev/null +++ b/python-2.7.14-1.build.sh @@ -0,0 +1,178 @@ +#! /bin/bash + +PKG=python +VERSION=2.7.14 +BUILD=1 + +PREFIX=/pkg/$PKG-$VERSION-$BUILD +#PREFIX=/dev/shm/$PKG-$VERSION-$BUILD + +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 $BUILDDIR + +URL=https://www.python.org/ftp/python/$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 + +( + cd build + test -e bx-python-0.7.2.tar.gz || wget https://pypi.python.org/packages/source/b/bx-python/bx-python-0.7.2.tar.gz + test -d bx-python-0.7.2 || tar xf bx-python-0.7.2.tar.gz + cd bx-python-0.7.2 + + patch -p1 <<'EOF2' +From 6515b765861be47ce64d28605df9fce0b6e47ecc Mon Sep 17 00:00:00 2001 +From: Donald Buczek +Date: Fri, 12 Jun 2015 12:12:35 +0200 +Subject: [PATCH] x + +--- + setup.py | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/setup.py b/setup.py +index 4ed8f19..72b5a44 100644 +--- a/setup.py ++++ b/setup.py +@@ -5,8 +5,8 @@ if sys.version_info < (2, 4): + sys.exit() + + # Automatically download setuptools if not available +-from distribute_setup import use_setuptools +-use_setuptools() ++#from distribute_setup import use_setuptools ++#use_setuptools() + + from setuptools import * + from glob import glob +-- +2.4.1 + +EOF2 + python setup.py install +) + +pip install Cython # for metaseq +pip install pycurl # for metaseq +pip install metaseq + +pip install macs2 +pip install HTSeq + +# for sasse: Theano and tensorflow (cuda version) + +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 + +function plaininstall() { + local dir=$1 + local tar=$2 + local url=$3 + ( + cd build + test -e $tar || wget $url + test -d $dir || tar xvf $tar + cd $dir + ./configure --prefix=$PREFIX + make -j $(nproc) + make install + ) +} + +# for Klages +# +pip install GPy distribute h5py igraph ranger pep8 +plaininstall pygtk-2.24.0 pygtk-2.24.0.tar.gz https://ftp.gnome.org/pub/GNOME/sources/pygtk/2.24/pygtk-2.24.0.tar.gz +plaininstall pygobject-2.28.7 pygobject-2.28.7.tar.xz https://ftp.gnome.org/pub/gnome/sources/pygobject/2.28/pygobject-2.28.7.tar.xz +plaininstall pygtksourceview-2.10.1 pygtksourceview-2.10.1.tar.gz https://ftp.gnome.org/pub/gnome/sources/pygtksourceview/2.10/pygtksourceview-2.10.1.tar.gz +# dbus-python: from 1.2.0 on 'Requested 'dbus-1 >= 1.6' but version of dbus is 1.4.0' +plaininstall dbus-python-1.1.1 dbus-python-1.1.1.tar.gz https://dbus.freedesktop.org/releases/dbus-python/dbus-python-1.1.1.tar.gz + +( + cd build + test -e py2cairo-1.10.0.tar.gz || wget https://www.cairographics.org/releases/py2cairo-1.10.0.tar.bz2 + test -d py2cairo-1.10.0 || tar xf py2cairo-1.10.0.tar.bz2 + cd py2cairo-1.10.0 + ./waf configure --prefix=$PREFIX + ./waf build + ./waf install +) + +pip install keras +pip install deeptools # Alene vom Boemmel -> helpdesk 19.04.2017 + +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 + +# Helpdesk 01/23/18 21:43, Sabrina Krakau +# pip install umi-tools # see above +pip install cutadapt + +# exit 1 # final test, inhibits 'closing' on success +exit