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python: Add version 3.7.1
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Almost the same packages as in 3.6.6, 'metaseq' fails, and
'hic2cool' was added.
Snakemake fails due to a single dependency, so maybe next turn.
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thomas committed Nov 5, 2018
1 parent 5215fe7 commit b5e87b4
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99 changes: 99 additions & 0 deletions python-3.7.1-0.build.sh
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#! /bin/sh

set -xe

PKG=python
VERSION=3.7.1
BUILD=0
PREFIX=/pkg/$PKG-$VERSION-$BUILD
# PREFIX=/dev/shm/pkg/$PKG-$VERSION-$BUILD

PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
export PATH

exec </dev/null

mkdir -p $PREFIX
cat >$PREFIX/profile <<-EOF
PATH=$PREFIX/bin:\$PATH
EOF
. $PREFIX/profile

mkdir -p $PREFIX/build
cd $PREFIX/build

# if false; then ########################## DEBUG #########
# fi ########################## DEBUG #########

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
./configure \
--prefix=$PREFIX
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 $SIP_SRC
# test -n 'XWIPE' && rm -rf sip-$SIP_VERSION
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

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
# pip3 install snakemake # fails

# 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+

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

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