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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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#! /bin/sh | ||
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set -xe | ||
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PKG=python | ||
VERSION=3.7.1 | ||
BUILD=0 | ||
PREFIX=/pkg/$PKG-$VERSION-$BUILD | ||
# PREFIX=/dev/shm/pkg/$PKG-$VERSION-$BUILD | ||
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PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin | ||
export PATH | ||
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exec </dev/null | ||
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mkdir -p $PREFIX | ||
cat >$PREFIX/profile <<-EOF | ||
PATH=$PREFIX/bin:\$PATH | ||
EOF | ||
. $PREFIX/profile | ||
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mkdir -p $PREFIX/build | ||
cd $PREFIX/build | ||
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# if false; then ########################## DEBUG ######### | ||
# fi ########################## DEBUG ######### | ||
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test -e Python-$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 | ||
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( # 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 | ||
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PYTHONVER=$( echo $VERSION | cut -f 1-2 -d. ) | ||
cd sip-$SIP_VERSION | ||
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python3 configure.py \ | ||
-b $PREFIX/bin \ | ||
-d $PREFIX/lib/python$PYTHONVER/site-packages \ | ||
-e $PREFIX/include/python${PYTHONVER}m \ | ||
-v $PREFIX/share/sip | ||
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mkdir -p $PREFIX/share/sip | ||
make; make install | ||
) | ||
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python3 -m ensurepip | ||
pip3 install -I pip | ||
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pip3 install ipython[all] | ||
pip3 install SciPy NumPy Matplotlib pandas SymPy nose statsmodels | ||
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pip3 install Cython | ||
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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 | ||
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# Helpdesk 01/24/18 16:19, Sabrina Krakau | ||
pip3 install cutadapt | ||
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#Helpdesk 03/26/18 14:19, Virginie Stanisla | ||
pip3 install pygobject | ||
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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 | ||
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# Alena 30.8.2018 | ||
pip3 install MotifScan | ||
pip3 install MAmotif | ||
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pip3 install hic2cool # helpdesk robert schoepflin 17.09.2018 | ||
# pip3 install hifive # only 2.7+ | ||
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# exit 1 # final test, inhibits 'closing' on success | ||
exit |