Update python 3.7

python-3.7.3-0.build.sh

@@ -0,0 +1,128 @@
+#! /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