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executable file 128 lines (100 sloc) 3.21 KB
#! /bin/bash
PKG=python
VERSION=3.7.3
BUILD=0
PREFIX=/pkg/$PKG-$VERSION-$BUILD
if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
set -xe
umask 022
BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp
test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; 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
if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi
EOF
. $PREFIX/profile
export MAKEFLAGS="-j $(nproc)"
BUILDDIR=$PREFIX/build
mkdir -p $BUILDDIR
cd $BUILDDIR
test -e Python-$VERSION.tar.xz || wget https://www.python.org/ftp/python/$VERSION/Python-$VERSION.tar.xz
test -d Python-$VERSION || tar xvf Python-$VERSION.tar.xz
cd Python-$VERSION
LDFLAGS="-Wl,-rpath=$PREFIX/lib" \
./configure \
--prefix=$PREFIX \
--enable-shared
make -j $(nproc)
# make test || true # 'test_socket' seems to run for ever
make install
( # sip: tool to create Python bindings for C and C++ libraries.
cd $PREFIX/build
SIP_VERSION=4.19.13
SIP_SRC=https://sourceforge.net/projects/pyqt/files/sip/sip-$SIP_VERSION/sip-$SIP_VERSION.tar.gz
test -e sip-$SIP_VERSION.tar.gz || wget $SIP_SRC
test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz
PYTHONVER=$( echo $VERSION | cut -f 1-2 -d. )
cd sip-$SIP_VERSION
python3 configure.py \
-b $PREFIX/bin \
-d $PREFIX/lib/python$PYTHONVER/site-packages \
-e $PREFIX/include/python${PYTHONVER}m \
-v $PREFIX/share/sip
mkdir -p $PREFIX/share/sip
make; make install
)
python3 -m ensurepip
pip3 install -I pip
pip3 install ipython[all]
pip3 install SciPy NumPy Matplotlib pandas SymPy nose statsmodels
pip3 install Cython
pip3 install pysam
pip3 install seaborn
pip3 install scikit-learn
# pip3 install metaseq # fails (Latest commit fa875d1 on Jan 10, 2017)
pip3 install Mako
pip3 install meson
# Helpdesk 01/24/18 16:19, Sabrina Krakau
pip3 install cutadapt
#Helpdesk 03/26/18 14:19, Virginie Stanisla
pip3 install pygobject
# Blink1-lib 07/04/18 12:00, Niclas Hofmann
pip3 install blink1
pip3 install python-bioformats
pip3 install umi-tools
pip3 install sphinx
pip3 install recommonmark
pip3 install fastcluster
pip3 install pydot
pip3 install pygraphviz
pip3 install deeptools
pip3 install HTSeq
pip3 install keras
# Alena 30.8.2018
pip3 install MotifScan
pip3 install MAmotif
pip3 install hic2cool # helpdesk robert schoepflin 17.09.2018
# pip3 install hifive # only 2.7+
# snakemake likes to have this one, but datrie isn't 3.7 aware ...
# luckily a fix is available (https://github.com/pytries/datrie/issues/52)
(
DATRIE_PY_VERSION=0.7.1
DATRIE_PY_SRC=https://github.com/pytries/datrie/archive/$DATRIE_PY_VERSION.tar.gz
cd $PREFIX/build
test -e $DATRIE_PY_VERSION.tar.gz || wget $DATRIE_PY_SRC
test -d datrie-$DATRIE_PY_VERSION || tar -xf $DATRIE_PY_VERSION.tar.gz
cd datrie-$DATRIE_PY_VERSION
./update_c.sh
python3.7 setup.py build
python3.7 setup.py install
)
pip3 install snakemake
pip3 install virtualenv # Donald
pip3 install odfpy # Donald
pip3 install Dumper # Thomas
exit