From b5e87b4d7b474195546cc35a1f237344c097ec2e Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Mon, 5 Nov 2018 14:42:26 +0100
Subject: [PATCH] python: Add version 3.7.1

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.
---
 python-3.7.1-0.build.sh | 99 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100755 python-3.7.1-0.build.sh

diff --git a/python-3.7.1-0.build.sh b/python-3.7.1-0.build.sh
new file mode 100755
index 0000000..c2cf69d
--- /dev/null
+++ b/python-3.7.1-0.build.sh
@@ -0,0 +1,99 @@
+#! /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