python-2.7.14-1: Rebuild due to buggy pyBigWig

  Added: cutadapt, request from Sabrina Krakau

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 </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 $BUILDDIR
+
+URL=https://www.python.org/ftp/python/$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
+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