python-2.7.14-2.build.sh

#! /bin/bash

PKG=python
VERSION=2.7.14
BUILD=2

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 </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

(
	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 <buczek@molgen.mpg.de>
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,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=0.7.5
	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
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

pip install cutadapt   # Sabrina Krakau,  23.01.2018 (phd Seminar)
pip install umi-tools  # Sabrina Krakau,  23.01.2018 (phd Seminar)

# to be removed from system. Install here:

plaininstall libxml2-2.9.4 libxml2-2.9.4.tar.gz http://xmlsoft.org/sources/libxml2-2.9.4.tar.gz
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
)

# exit 1 # final test, inhibits 'closing' on success
exit