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executable file 277 lines (220 sloc) 7.65 KB
#! /bin/bash
PKG=python
VERSION=2.7.15
BUILD=2
PREFIX=/pkg/$PKG-$VERSION-$BUILD
# PREFIX=/dev/shm/pkg/$PKG-$VERSION-$BUILD
XPYTHONVER=2.7
XPYTHONLIB=$PREFIX/lib/python$XPYTHONVER/site-packages
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=$PREFIX/bin:\$PATH
PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH}
export PKG_CONFIG_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' > $BUILDDIR/dont_clobber_numpy_on_linux
pip install tensorflow-gpu --constraint $BUILDDIR/dont_clobber_numpy_on_linux
pip install biopython # wird von bressin fuer python3 benutzt. klingt gut, ist in metaseq requirement drin
pip install git+git://github.com/tanghaibao/jcvi.git # angefragt von Dr. Jun Yang
# for Klages
#
# we need cairo otherwise pygtk won't do the gtk stuff and pygtk.h
# if we install cairo with wheel, we dont get a pkg-config file.
pip install --no-binary :all: pycairo
pip install GPy distribute h5py igraph ranger pep8
plaininstall pygobject-2.28.7 pygobject-2.28.7.tar.xz https://ftp.gnome.org/pub/gnome/sources/pygobject/2.28/pygobject-2.28.7.tar.xz
plaininstall pygtk-2.24.0 pygtk-2.24.0.tar.gz https://ftp.gnome.org/pub/GNOME/sources/pygtk/2.24/pygtk-2.24.0.tar.gz
# no new packages since apr 2010
plaininstall pygtksourceview-2.10.1 pygtksourceview-2.10.1.tar.gz https://ftp.gnome.org/pub/gnome/sources/pygtksourceview/2.10/pygtksourceview-2.10.1.tar.gz
plaininstall dbus-python-1.2.8 dbus-python-1.2.8.tar.gz https://dbus.freedesktop.org/releases/dbus-python/dbus-python-1.2.8.tar.gz
(
cd build
# nothing new since Apr 2011
test -e py2cairo-1.10.0.tar.gz || wget https://www.cairographics.org/releases/py2cairo-1.10.0.tar.bz2
test -d py2cairo-1.10.0 || tar xf py2cairo-1.10.0.tar.bz2
cd py2cairo-1.10.0
./waf configure --prefix=$PREFIX
./waf build
./waf install
)
pip install keras
pip install deeptools # Alena 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 > $BUILDDIR/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
# setup.py bdist_wheel for HiCExplorer fails, but setup.py install
# creates a working executable, so don't get confused.
pip install HiCExplorer --constraint $BUILDDIR/such_a_lamer --no-warn-conflicts
(
SIP_VERSION=4.19.13
SIP_SRC=https://sourceforge.net/projects/pyqt/files/sip/sip-$SIP_VERSION/sip-$SIP_VERSION.tar.gz
cd $BUILDDIR
test -e sip-$SIP_VERSION.tar.gz || wget $SIP_SRC
test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz
cd sip-$SIP_VERSION
python configure.py\
-b $PREFIX/bin \
-d $XPYTHONLIB \
-e $PREFIX/include/python$XPYTHONVER \
-v $PREFIX/share/sip
mkdir -p $PREFIX/share/sip
make; make install
)
(
# Don't use 5.11.3 !
PYQT_VERSION=5.10.1
PYQT_SRC=https://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-$PYQT_VERSION/PyQt5_gpl-$PYQT_VERSION.tar.gz
cd $BUILDDIR
test -e PyQt5_gpl-$PYQT_VERSION.tar.gz || wget $PYQT_SRC
test -d PyQt5_gpl-$PYQT_VERSION || tar -xf PyQt5_gpl-$PYQT_VERSION.tar.gz
cd PyQt5_gpl-$PYQT_VERSION
export QTDIR=/usr/local/qt5
python configure.py \
-b $PREFIX/bin \
-d $XPYTHONLIB \
-q /usr/local/qt5/bin/qmake \
-v $PREFIX/share/sip \
--confirm-license \
--no-designer-plugin \
--no-python-dbus \
--no-qml-plugin \
--no-stubs \
--sip-incdir=$PREFIX/include/python$XPYTHONVER \
--verbose
make -j $(nproc); make install
)
cp -pr $PREFIX/man $PREFIX/share
rm -r $PREFIX/man
# exit 1 # final test, inhibits 'closing' on success
exit