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pkg-scripts/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 |