From e129431f61b72d88e60c18c1588a85c8ffb9f81c Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Fri, 27 Mar 2020 10:10:59 +0100
Subject: [PATCH 01/18] Revert "Python-3.7.6: Add package from
 https://github.molgen.mpg.de/mariux64/pkg-scripts/pull/104/files"

This reverts commit 10307f6bd8f31334481da882fef57bbfd8d5b35d.

The commit has been added to the master branch by accident. Remove it.
---
 python-3.7.6-0.build.sh | 330 ----------------------------------------
 1 file changed, 330 deletions(-)
 delete mode 100644 python-3.7.6-0.build.sh

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
deleted file mode 100644
index 186ee89..0000000
--- a/python-3.7.6-0.build.sh
+++ /dev/null
@@ -1,330 +0,0 @@
-#! /bin/bash
-
-COOKIE=$(mcookie); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 1; exec bash /dev/shm/runme-$COOKIE.sh $1
-
-
-PKG=python
-VERSION=3.7.6
-BUILD=0
-PYTHONVER=${VERSION%.*}
-
-CUDADIR=/pkg/cuda-10.1.105-0
-
-PREFIX=/pkg/$PKG-$VERSION-$BUILD
-if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
-
-PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
-
-set -xe
-umask 022
-
-BUILD_TMPDIR=/dev/shm/$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
-	\. $CUDADIR/profile
-	PATH=$PREFIX/bin:\$PATH
-	export LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH
-	export PYTHONPATH=$PREFIX/lib/python3.7/site-packages\${PYTHONPATH:+:}\$PYTHONPATH
-	PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH}
-	export PKG_CONFIG_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 $PREFIX/build
-  SIP_VERSION=4.19.18
-  SIP_SRC=https://www.riverbankcomputing.com/static/Downloads/sip/$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-$SIP_VERSION.tar.gz
-
-  cd sip-$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 \
-      --sip-module=sip
-
-  # well, right here share/sip is spoilage, but maybe some packages will use the decent sip later on ...
-  mkdir -p $PREFIX/share/sip
-  make -j $(nproc);
-  make install
-)
-
-
-( # now for the private (sic!) version required by newer PyQt
-  cd $PREFIX/build
-  mkdir -p private_sip
-  cd private_sip
-  SIP_VERSION=4.19.18
-  SIP_SRC=https://www.riverbankcomputing.com/static/Downloads/sip/$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-$SIP_VERSION.tar.gz
-
-  cd sip-$SIP_VERSION
-
-  # note $PREFIX/share/sip/PyQt5 is mandatory
-  python3 configure.py \
-      -d $PREFIX/lib/python$PYTHONVER/site-packages \
-      -v $PREFIX/share/sip/PyQt5 \
-      --no-tools \
-      --sip-module=PyQt5.sip
-
-  mkdir -p $PREFIX/share/sip/PyQt5
-  make -j $(nproc)
-  # The resulting sip.so in site-packages/PyQt5 differs indeed a bit (grep for PyQt5)
-  make install
-)
-
-(
-  PYQT_VERSION=5.13.0
-  PYQT_SRC=https://www.riverbankcomputing.com/static/Downloads/PyQt5/$PYQT_VERSION/PyQt5_gpl-$PYQT_VERSION.tar.gz
-
-  cd $BUILDDIR
-  test -e PyQt5_gpl-$PYQT_VERSION.tar.gz || wget $PYQT_SRC
-  test -d PyQt5_gpl-$PYQT_VERSION || tar -xf PyQt5_gpl-$PYQT_VERSION.tar.gz
-
-  cd PyQt5_gpl-$PYQT_VERSION
-
-  # export QTDIR=/usr/local/qt5
-  python3 configure.py \
-    -b $PREFIX/bin \
-    -d $PREFIX/lib/python$PYTHONVER/site-packages \
-    -n $PREFIX/share/qsci \
-    -q /usr/local/qt5/bin/qmake \
-    -v $PREFIX/share/sip/PyQt5 \
-    --sip-incdir=$PREFIX/include/python${PYTHONVER}m \
-    --confirm-license \
-    --no-qml-plugin \
-    --no-designer-plugin \
-    --no-dist-info \
-    --verbose
-
-  make -j $(nproc)
-
-  # Did I miss something in the docs ???
-  # w/o the *.so files inplace a clean 'make install' fails with file not found ...
-  # -> FileNotFoundError: [Errno 2] No such file or directory:
-  #         '/dev/shm/python-3.7.4-0/lib/python3.7/site-packages/PyQt5/QtCore.so'
-  mkdir -p $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
-  for F in `find | grep '\.so$' | grep -v '/lib'` ; do
-    cp -vp $F $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5/
-  done
-  make install
-)
-
-(
-  QSCINTILLA_VERSION=2.11.2
-  QSCINTILLA_SRC=https://www.riverbankcomputing.com/static/Downloads/QScintilla/$QSCINTILLA_VERSION/QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz
-
-  cd $BUILDDIR
-  test -e QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz || wget $QSCINTILLA_SRC
-  test -d QScintilla_gpl-$QSCINTILLA_VERSION || tar -xf QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz
-  cd QScintilla_gpl-$QSCINTILLA_VERSION
-
-  cd Python
-
-  # apidir follows PyQt, not Qt (default is: QT_INSTALL_DATA/qsci)
-  # creation of PEP 376 .dist-info fails in $PREFIX/share
-  python3 configure.py \
-    --pyqt=PyQt5 \
-    --qmake=/usr/local/qt5/bin/qmake \
-    --apidir=$PREFIX/share/qsci \
-    --no-dist-info
-
-  make -j $(nproc)
-
-  # Call it a deja-vu, nerve ...
-  # -> FileNotFoundError: [Errno 2] No such file or directory: '/dev/shm/python-3.7.4-0/lib/python3.7/site-packages/PyQt5/Qsci.so'
-  mkdir -p $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
-  for F in `find | grep '\.so$' | grep -v '/lib'` ; do
-    cp -vp $F $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
-  done
-  make install
-)
-
-python3 -m ensurepip
-pip3 install --prefix=$PREFIX -I pip
-
-pip3 install --prefix=$PREFIX ipython[all]
-
-pip3 install --prefix=$PREFIX SciPy NumPy Matplotlib pandas SymPy nose statsmodels
-# clean up some dirt that statsmodels placed also into $PREFIX
-rm -vf $PREFIX/LICENSE.txt
-rm -vf $PREFIX/setup.cfg
-
-pip3 install --prefix=$PREFIX Cython
-
-pip3 install --prefix=$PREFIX pysam
-pip3 install --prefix=$PREFIX seaborn
-pip3 install --prefix=$PREFIX scikit-learn
-#pip3 install --prefix=$PREFIX metaseq      # fails (Latest commit fa875d1 on Jan 10, 2017)
-pip3 install --prefix=$PREFIX Mako
-pip3 install --prefix=$PREFIX meson          # required in mariux
-
-pip3 install --prefix=$PREFIX cutadapt       # Helpdesk 01/24/18 16:19, Sabrina Krakau
-pip3 install --prefix=$PREFIX pygobject      # Helpdesk 03/26/18 14:19, Virginie Stanisla
-pip3 install --prefix=$PREFIX blink1         # Blink1-lib 07/04/18 12:00, Niclas Hofmann
-
-pip3 install --prefix=$PREFIX umi-tools
-pip3 install --prefix=$PREFIX sphinx
-pip3 install --prefix=$PREFIX recommonmark
-pip3 install --prefix=$PREFIX fastcluster
-pip3 install --prefix=$PREFIX pydot
-pip3 install --prefix=$PREFIX pygraphviz
-pip3 install --prefix=$PREFIX deeptools
-pip3 install --prefix=$PREFIX HTSeq
-pip3 install --prefix=$PREFIX keras
-pip3 install --prefix=$PREFIX MotifScan      # Alena 30.8.2018
-pip3 install --prefix=$PREFIX MAmotif
-#pip3 install --prefix=$PREFIX hic2cool       # Helpdesk Robert Schoepflin 17.09.2018 Would be a nice to have, but it likes to downgrade too much, pick some cherries
-#pip3 install --prefix=$PREFIX hifive       # only python 2.7+
-pip3 install --prefix=$PREFIX snakemake
-pip3 install --prefix=$PREFIX virtualenv     # Donald
-pip3 install --prefix=$PREFIX odfpy          # Donald
-pip3 install --prefix=$PREFIX Dumper         # Thomas
-pip3 install --prefix=$PREFIX igraph
-pip3 install --prefix=$PREFIX louvain        # monocle3 prep for Helene
-pip3 install --prefix=$PREFIX selenium       # 19.7.19 Kreitler  -> https://webxray.org/
-pip3 install --prefix=$PREFIX cooltools      # Maria Valieva 17.7.2019
-pip3 install --prefix=$PREFIX gmpy           # From viper context (Helpdesk Laura Glaser 9.8.2019)
-pip3 install --prefix=$PREFIX tensorflow==2.0.1         # tensorflow-2.1.0 needs spezial libs and nightly version(2.2.0) dont
-pip3 install --prefix=$PREFIX torch
-pip3 install --prefix=$PREFIX torchvision
-pip3 install --prefix=$PREFIX plotly
-pip3 install --prefix=$PREFIX pyOpenCL
-pip3 install --prefix=$PREFIX docopt
-pip3 install --prefix=$PREFIX dbus-python
-pip3 install --prefix=$PREFIX distro
-pip3 install --prefix=$PREFIX notify
-pip3 install --prefix=$PREFIX ply
-pip3 install --prefix=$PREFIX threadpoolctl
-
-pip3 install --prefix=$PREFIX pyopengl
-rm -rf ${PREFIX}/lib/python$PYTHONVER/site-packages/OpenGL/Tk
-# create error, so remove it
-
-# pip3 install --prefix=$PREFIX HiCExplorer  # Would be a nice to have, but it likes to downgrade too much, pick some cherries
-pip3 install --prefix=$PREFIX HiCMatrix
-pip3 install --prefix=$PREFIX pyGenomeTracks
-
-pip3 install --prefix=$PREFIX python-bioformats
-
-pip3 install --prefix=$PREFIX jupyterlab      # request Peter Arndt
-pip3 install --prefix=$PREFIX jupyterlab-git
-pip3 install --prefix=$PREFIX libxml2-python3 # required by several bee packages after swich to python3
-pip3 install --prefix=$PREFIX scour           # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98
-
-#boost for pycuda
-(
-	. ${PREFIX}/profile
-	BOOST_VERSION="1.72.0 1_72_0"
-	BOOST_SRC=https://dl.bintray.com/boostorg/release/$( echo $BOOST_VERSION | cut -d" " -f1 )/source/boost_$( echo $BOOST_VERSION | cut -d" " -f2 ).tar.gz
-	PKGCFLAGS="-O2 -fPIC"
-
-	cd $BUILDDIR
-	test -e boost_$( echo $BOOST_VERSION | cut -d" " -f2 ).tar.gz || wget $BOOST_SRC
-	test -d boost-$( echo $BOOST_VERSION | cut -d" " -f1 ) || mkdir boost-$( echo $BOOST_VERSION | cut -d" " -f1 ) && tar -xf boost_$( echo $BOOST_VERSION | cut -d" " -f2 ).tar.gz -C boost-$( echo $BOOST_VERSION | cut -d" " -f1 ) --strip-components=1
-
-	cd boost-$( echo $BOOST_VERSION | cut -d" " -f1 )
-	sed -e "/using python/ s|;|: ${PREFIX}/include/python${PYTHONVER}m ;|" \
-      -i bootstrap.sh
-
-	./bootstrap.sh \
-    --with-toolset=gcc \
-    --with-icu \
-    --with-python=$PREFIX/bin/python3 \
-    --with-libraries=python,thread || exit 1
-
-	./b2 \
-    $NUMJOBS \
-    --layout=system \
-    --build-dir=build-python3 \
-    --prefix=$PREFIX \
-    --libdir=$PREFIX/lib \
-    --build-type=minimal \
-    toolset=gcc \
-    variant=release \
-    debug-symbols=off \
-    link=shared \
-    threading=multi \
-    runtime-link=shared \
-    python=$PYTHONVER \
-    cflags="$PKGCFLAGS" \
-    cxxflags="$PKGCFLAGS" \
-    stage || exit 1
-
-  ./b2 \
-    $NUMJOBS \
-    --layout=system \
-    --build-dir=build-python3 \
-    --prefix=$PREFIX \
-    --libdir=$PREFIX/lib \
-    --build-type=minimal \
-    toolset=gcc \
-    variant=release \
-    debug-symbols=off \
-    link=shared \
-    threading=multi \
-    runtime-link=shared \
-    python=$PYTHONVER \
-    cflags="$PKGCFLAGS" \
-    cxxflags="$PKGCFLAGS" \
-    install || exit 1
-)
-
-#pycuda git version to get GL support
-(
-	. ${PREFIX}/profile
-	cd $BUILDDIR
-	test -d pycuda || git clone --recursive http://git.tiker.net/trees/pycuda.git
-
-	cd pycuda
-	git clean -dffx
-	python3 configure.py \
-    --cuda-enable-gl \
-    --cuda-root=$CUDADIR \
-    --no-use-shipped-boost \
-    --boost-python-libname=boost_python37 \
-    --boost-inc-dir=$PREFIX/include \
-    --boost-lib-dir=$PREFIX/lib \
-    --cudadrv-lib-dir='${CUDA_ROOT}/lib64,${CUDA_ROOT}/lib64/stubs' \
-    --cudart-lib-dir='${CUDA_ROOT}/lib64,${CUDA_ROOT}/lib64/stubs' \
-    --curand-lib-dir='${CUDA_ROOT}/lib64,${CUDA_ROOT}/lib64/stubs'\
-    --ldflags=-L$PREFIX/lib
-
-	python3 setup.py install --prefix $PREFIX
-)
-# try to load all packages, maybe we can see installation errors
-python3 -c 'help("modules")' > /dev/null
-
-exit

From 73210ab3099d6e119452ccad8cfdb9ee19a388b8 Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Fri, 27 Mar 2020 10:14:06 +0100
Subject: [PATCH 02/18] Add python-3.7.6

Create bee file with

    cp python-3.7.4-2.build.sh python-3.7.6-0.build.sh

and update version and build number.
---
 python-3.7.6-0.build.sh | 221 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 221 insertions(+)
 create mode 100755 python-3.7.6-0.build.sh

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
new file mode 100755
index 0000000..e57e0c7
--- /dev/null
+++ b/python-3.7.6-0.build.sh
@@ -0,0 +1,221 @@
+#! /bin/bash
+
+PKG=python
+VERSION=3.7.6
+BUILD=0
+PYTHONVER=${VERSION%.*}
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
+
+PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
+
+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=$PREFIX/bin:\$PATH
+	PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH}
+	export PKG_CONFIG_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 $PREFIX/build
+  SIP_VERSION=4.19.18
+  SIP_SRC=https://www.riverbankcomputing.com/static/Downloads/sip/$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-$SIP_VERSION.tar.gz
+
+  cd sip-$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 \
+      --sip-module=sip
+
+  # well, right here share/sip is spoilage, but maybe some packages will use the decent sip later on ...
+  mkdir -p $PREFIX/share/sip
+  make -j $(nproc);
+  make install
+)
+
+
+( # now for the private (sic!) version required by newer PyQt
+  cd $PREFIX/build
+  mkdir -p private_sip
+  cd private_sip
+  SIP_VERSION=4.19.18
+  SIP_SRC=https://www.riverbankcomputing.com/static/Downloads/sip/$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-$SIP_VERSION.tar.gz
+
+  cd sip-$SIP_VERSION
+
+  # note $PREFIX/share/sip/PyQt5 is mandatory
+  python3 configure.py \
+      -d $PREFIX/lib/python$PYTHONVER/site-packages \
+      -v $PREFIX/share/sip/PyQt5 \
+      --no-tools \
+      --sip-module=PyQt5.sip
+
+  mkdir -p $PREFIX/share/sip/PyQt5
+  make -j $(nproc)
+  # The resulting sip.so in site-packages/PyQt5 differs indeed a bit (grep for PyQt5)
+  make install
+)
+
+(
+  PYQT_VERSION=5.13.0
+  PYQT_SRC=https://www.riverbankcomputing.com/static/Downloads/PyQt5/$PYQT_VERSION/PyQt5_gpl-$PYQT_VERSION.tar.gz
+
+  cd $BUILDDIR
+  test -e PyQt5_gpl-$PYQT_VERSION.tar.gz || wget $PYQT_SRC
+  test -d PyQt5_gpl-$PYQT_VERSION || tar -xf PyQt5_gpl-$PYQT_VERSION.tar.gz
+
+  cd PyQt5_gpl-$PYQT_VERSION
+
+  # export QTDIR=/usr/local/qt5
+  python3 configure.py \
+    -b $PREFIX/bin \
+    -d $PREFIX/lib/python$PYTHONVER/site-packages \
+    -n $PREFIX/share/qsci \
+    -q /usr/local/qt5/bin/qmake \
+    -v $PREFIX/share/sip/PyQt5 \
+    --sip-incdir=$PREFIX/include/python${PYTHONVER}m \
+    --confirm-license \
+    --no-qml-plugin \
+    --no-designer-plugin \
+    --no-dist-info \
+    --verbose
+
+  make -j $(nproc)
+
+  # Did I miss something in the docs ???
+  # w/o the *.so files inplace a clean 'make install' fails with file not found ...
+  # -> FileNotFoundError: [Errno 2] No such file or directory:
+  #         '/dev/shm/python-3.7.4-0/lib/python3.7/site-packages/PyQt5/QtCore.so'
+  mkdir -p $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
+  for F in `find | grep '\.so$' | grep -v '/lib'` ; do
+    cp -vp $F $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5/
+  done
+  make install
+)
+
+(
+  QSCINTILLA_VERSION=2.11.2
+  QSCINTILLA_SRC=https://www.riverbankcomputing.com/static/Downloads/QScintilla/$QSCINTILLA_VERSION/QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz
+
+  cd $BUILDDIR
+  test -e QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz || wget $QSCINTILLA_SRC
+  test -d QScintilla_gpl-$QSCINTILLA_VERSION || tar -xf QScintilla_gpl-$QSCINTILLA_VERSION.tar.gz
+  cd QScintilla_gpl-$QSCINTILLA_VERSION
+
+  cd Python
+
+  # apidir follows PyQt, not Qt (default is: QT_INSTALL_DATA/qsci)
+  # creation of PEP 376 .dist-info fails in $PREFIX/share
+  python3 configure.py \
+    --pyqt=PyQt5 \
+    --qmake=/usr/local/qt5/bin/qmake \
+    --apidir=$PREFIX/share/qsci \
+    --no-dist-info
+
+  make -j $(nproc)
+
+  # Call it a deja-vu, nerve ...
+  # -> FileNotFoundError: [Errno 2] No such file or directory: '/dev/shm/python-3.7.4-0/lib/python3.7/site-packages/PyQt5/Qsci.so'
+  mkdir -p $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
+  for F in `find | grep '\.so$' | grep -v '/lib'` ; do
+    cp -vp $F $PREFIX/lib/python$PYTHONVER/site-packages/PyQt5
+  done
+  make install
+)
+
+python3 -m ensurepip
+pip3 install -I pip
+
+pip3 install ipython[all]
+
+pip3 install SciPy NumPy Matplotlib pandas SymPy nose statsmodels
+# clean up some dirt that statsmodels placed also into $PREFIX
+rm -vf $PREFIX/LICENSE.txt
+rm -vf $PREFIX/setup.cfg
+
+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          # required in mariux
+
+pip3 install cutadapt       # Helpdesk 01/24/18 16:19, Sabrina Krakau
+pip3 install pygobject      # Helpdesk 03/26/18 14:19, Virginie Stanisla
+pip3 install blink1         # Blink1-lib 07/04/18 12:00, Niclas Hofmann
+
+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 MotifScan      # Alena 30.8.2018
+pip3 install MAmotif
+pip3 install hic2cool       # Helpdesk Robert Schoepflin 17.09.2018
+# pip3 install hifive       # only python 2.7+
+pip3 install snakemake
+pip3 install virtualenv     # Donald
+pip3 install odfpy          # Donald
+pip3 install Dumper         # Thomas
+pip3 install igraph
+pip3 install louvain        # monocle3 prep for Helene
+pip3 install selenium       # 19.7.19 Kreitler  -> https://webxray.org/
+pip3 install cooltools      # Maria Valieva 17.7.2019
+pip3 install gmpy           # From viper context (Helpdesk Laura Glaser 9.8.2019)
+
+# pip3 install HiCExplorer  # Would be a nice to have, but it likes to downgrade too much, pick some cherries
+pip3 install HiCMatrix
+pip3 install pyGenomeTracks
+
+pip3 install python-bioformats
+
+pip3 install jupyterlab      # request Peter Arndt
+
+exit

From a37219c185bc671d552379259f603b8393d9788d Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Fri, 27 Mar 2020 11:37:46 +0100
Subject: [PATCH 03/18] python-3.7.6: Add --prefix to pip

If pip finds the system installation path not writable, it falls
back to --user and installs into ~/.local.

Of course, when this script runs, its system installation path should
be writable. However, other errors in our environment, which prevent
$PREFIX from being written to, might go undetected because of the
fallback.

Specify --prefix to abort if $PREFIX is not writable.
---
 python-3.7.6-0.build.sh | 92 ++++++++++++++++++++---------------------
 1 file changed, 46 insertions(+), 46 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index e57e0c7..694f684 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -165,57 +165,57 @@ make install
 )
 
 python3 -m ensurepip
-pip3 install -I pip
+pip3 install --prefix=$PREFIX -I pip
 
-pip3 install ipython[all]
+pip3 install --prefix=$PREFIX ipython[all]
 
-pip3 install SciPy NumPy Matplotlib pandas SymPy nose statsmodels
+pip3 install --prefix=$PREFIX SciPy NumPy Matplotlib pandas SymPy nose statsmodels
 # clean up some dirt that statsmodels placed also into $PREFIX
 rm -vf $PREFIX/LICENSE.txt
 rm -vf $PREFIX/setup.cfg
 
-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          # required in mariux
-
-pip3 install cutadapt       # Helpdesk 01/24/18 16:19, Sabrina Krakau
-pip3 install pygobject      # Helpdesk 03/26/18 14:19, Virginie Stanisla
-pip3 install blink1         # Blink1-lib 07/04/18 12:00, Niclas Hofmann
-
-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 MotifScan      # Alena 30.8.2018
-pip3 install MAmotif
-pip3 install hic2cool       # Helpdesk Robert Schoepflin 17.09.2018
-# pip3 install hifive       # only python 2.7+
-pip3 install snakemake
-pip3 install virtualenv     # Donald
-pip3 install odfpy          # Donald
-pip3 install Dumper         # Thomas
-pip3 install igraph
-pip3 install louvain        # monocle3 prep for Helene
-pip3 install selenium       # 19.7.19 Kreitler  -> https://webxray.org/
-pip3 install cooltools      # Maria Valieva 17.7.2019
-pip3 install gmpy           # From viper context (Helpdesk Laura Glaser 9.8.2019)
-
-# pip3 install HiCExplorer  # Would be a nice to have, but it likes to downgrade too much, pick some cherries
-pip3 install HiCMatrix
-pip3 install pyGenomeTracks
-
-pip3 install python-bioformats
-
-pip3 install jupyterlab      # request Peter Arndt
+pip3 install --prefix=$PREFIX Cython
+
+pip3 install --prefix=$PREFIX pysam
+pip3 install --prefix=$PREFIX seaborn
+pip3 install --prefix=$PREFIX scikit-learn
+#pip3 install --prefix=$PREFIX metaseq      # fails (Latest commit fa875d1 on Jan 10, 2017)
+pip3 install --prefix=$PREFIX Mako
+pip3 install --prefix=$PREFIX meson          # required in mariux
+
+pip3 install --prefix=$PREFIX cutadapt       # Helpdesk 01/24/18 16:19, Sabrina Krakau
+pip3 install --prefix=$PREFIX pygobject      # Helpdesk 03/26/18 14:19, Virginie Stanisla
+pip3 install --prefix=$PREFIX blink1         # Blink1-lib 07/04/18 12:00, Niclas Hofmann
+
+pip3 install --prefix=$PREFIX umi-tools
+pip3 install --prefix=$PREFIX sphinx
+pip3 install --prefix=$PREFIX recommonmark
+pip3 install --prefix=$PREFIX fastcluster
+pip3 install --prefix=$PREFIX pydot
+pip3 install --prefix=$PREFIX pygraphviz
+pip3 install --prefix=$PREFIX deeptools
+pip3 install --prefix=$PREFIX HTSeq
+pip3 install --prefix=$PREFIX keras
+pip3 install --prefix=$PREFIX MotifScan      # Alena 30.8.2018
+pip3 install --prefix=$PREFIX MAmotif
+pip3 install --prefix=$PREFIX hic2cool       # Helpdesk Robert Schoepflin 17.09.2018
+#pip3 install --prefix=$PREFIX hifive       # only python 2.7+
+pip3 install --prefix=$PREFIX snakemake
+pip3 install --prefix=$PREFIX virtualenv     # Donald
+pip3 install --prefix=$PREFIX odfpy          # Donald
+pip3 install --prefix=$PREFIX Dumper         # Thomas
+pip3 install --prefix=$PREFIX igraph
+pip3 install --prefix=$PREFIX louvain        # monocle3 prep for Helene
+pip3 install --prefix=$PREFIX selenium       # 19.7.19 Kreitler  -> https://webxray.org/
+pip3 install --prefix=$PREFIX cooltools      # Maria Valieva 17.7.2019
+pip3 install --prefix=$PREFIX gmpy           # From viper context (Helpdesk Laura Glaser 9.8.2019)
+
+# pip3 install --prefix=$PREFIX HiCExplorer  # Would be a nice to have, but it likes to downgrade too much, pick some cherries
+pip3 install --prefix=$PREFIX HiCMatrix
+pip3 install --prefix=$PREFIX pyGenomeTracks
+
+pip3 install --prefix=$PREFIX python-bioformats
+
+pip3 install --prefix=$PREFIX jupyterlab      # request Peter Arndt
 
 exit

From f030a1747a168603dc03b14da933010806bd053e Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Fri, 27 Mar 2020 11:56:08 +0100
Subject: [PATCH 04/18] python-3.7.6: Add help("modules") at end of build

Add

    python3 -c 'help("modules")'

at the end of build script. The idea is, that this command requires all
available modules to be loaded and would emmit error messages and
non-zero exist status in case of any errors in the installation.
---
 python-3.7.6-0.build.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 694f684..bac3d09 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -218,4 +218,7 @@ pip3 install --prefix=$PREFIX python-bioformats
 
 pip3 install --prefix=$PREFIX jupyterlab      # request Peter Arndt
 
+# try to load all packages, maybe we can see installation errors
+python3 -c 'help("modules")' > /dev/null
+
 exit

From 8a1a6e92fa5bfe9cf88f3b502ef9af0d5338454a Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Fri, 27 Mar 2020 11:37:46 +0100
Subject: [PATCH 05/18] python-3.7.6: Add some python packages

---
 python-3.7.6-0.build.sh | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index bac3d09..7874b45 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -209,6 +209,21 @@ pip3 install --prefix=$PREFIX louvain        # monocle3 prep for Helene
 pip3 install --prefix=$PREFIX selenium       # 19.7.19 Kreitler  -> https://webxray.org/
 pip3 install --prefix=$PREFIX cooltools      # Maria Valieva 17.7.2019
 pip3 install --prefix=$PREFIX gmpy           # From viper context (Helpdesk Laura Glaser 9.8.2019)
+pip3 install --prefix=$PREFIX tensorflow==2.0.1         # tensorflow-2.1.0 needs spezial libs and nightly version(2.2.0) dont
+pip3 install --prefix=$PREFIX torch
+pip3 install --prefix=$PREFIX torchvision
+pip3 install --prefix=$PREFIX plotly
+pip3 install --prefix=$PREFIX pyOpenCL
+pip3 install --prefix=$PREFIX docopt
+pip3 install --prefix=$PREFIX dbus-python
+pip3 install --prefix=$PREFIX distro
+pip3 install --prefix=$PREFIX notify
+pip3 install --prefix=$PREFIX ply
+pip3 install --prefix=$PREFIX threadpoolctl
+
+pip3 install --prefix=$PREFIX pyopengl
+rm -rf ${PREFIX}/lib/python$PYTHONVER/site-packages/OpenGL/Tk
+# creates error, so remove it
 
 # pip3 install --prefix=$PREFIX HiCExplorer  # Would be a nice to have, but it likes to downgrade too much, pick some cherries
 pip3 install --prefix=$PREFIX HiCMatrix
@@ -217,6 +232,10 @@ pip3 install --prefix=$PREFIX pyGenomeTracks
 pip3 install --prefix=$PREFIX python-bioformats
 
 pip3 install --prefix=$PREFIX jupyterlab      # request Peter Arndt
+pip3 install --prefix=$PREFIX jupyterlab-git
+pip3 install --prefix=$PREFIX libxml2-python3 # required by several bee packages after swich to python3
+pip3 install --prefix=$PREFIX scour           # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98
+pip3 install --prefix=$PREFIX multiqc
 
 # try to load all packages, maybe we can see installation errors
 python3 -c 'help("modules")' > /dev/null

From 54b5ee160dc2248028c28daef19f3d189a2882ec Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Thu, 26 Mar 2020 08:41:28 +0100
Subject: [PATCH 06/18] python-3.7.6: Add comments to have eye on the
 downgraders

---
 python-3.7.6-0.build.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 7874b45..9741975 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -227,9 +227,9 @@ rm -rf ${PREFIX}/lib/python$PYTHONVER/site-packages/OpenGL/Tk
 
 # pip3 install --prefix=$PREFIX HiCExplorer  # Would be a nice to have, but it likes to downgrade too much, pick some cherries
 pip3 install --prefix=$PREFIX HiCMatrix
-pip3 install --prefix=$PREFIX pyGenomeTracks
+pip3 install --prefix=$PREFIX pyGenomeTracks #downgrader cooler 0.8.7-> 0.8.5
 
-pip3 install --prefix=$PREFIX python-bioformats
+pip3 install --prefix=$PREFIX python-bioformats #downgrader matplotlib 3.2.0->3.1.1 docutils 0.16 -> 0.15.2
 
 pip3 install --prefix=$PREFIX jupyterlab      # request Peter Arndt
 pip3 install --prefix=$PREFIX jupyterlab-git

From 7ccba0b57266886b535beb2c7f64c152360ed69a Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Fri, 27 Mar 2020 11:23:30 +0100
Subject: [PATCH 07/18] python-3.7.6: Add CUDA profile

We are going to install pycuda into this package, which requires
cuda at compile- and runtime, so add the cuda package to this packages
environment.
---
 python-3.7.6-0.build.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 9741975..188369e 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -5,6 +5,8 @@ VERSION=3.7.6
 BUILD=0
 PYTHONVER=${VERSION%.*}
 
+CUDADIR=/pkg/cuda-10.2.89-1
+
 PREFIX=/pkg/$PKG-$VERSION-$BUILD
 if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
 
@@ -23,6 +25,7 @@ exec </dev/null
 
 mkdir -p $PREFIX
 cat >$PREFIX/profile <<-EOF
+	. $CUDADIR/profile
 	PATH=$PREFIX/bin:\$PATH
 	PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH}
 	export PKG_CONFIG_PATH

From 44d3f2f94a743805e3e0e569935ab5337cd115cf Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Fri, 27 Mar 2020 11:27:27 +0100
Subject: [PATCH 08/18] python-3.7.6: Add LD_LIBRARY_PATH

We are going to install Tensorflow into this package.

Tensorflow loads implementation libraries at runtime which need to be
found. Add LD_LIBRARY_PATH to avoid runtime errors like

    Traceback (most recent call last):
      File "/dev/shm/python-3.7.6-0/lib/python3.7/site-packages/tensorflow-2.1.0-py3.7-linux-x86_64.egg/tensorflow_core/python/pywrap_tensorflow.py", line 58, in <module>
        from tensorflow.python.pywrap_tensorflow_internal import *
      File "/dev/shm/python-3.7.6-0/lib/python3.7/site-packages/tensorflow-2.1.0-py3.7-linux-x86_64.egg/tensorflow_core/python/pywrap_tensorflow_internal.py", line 28, in <module>
        _pywrap_tensorflow_internal = swig_import_helper()
      File "/dev/shm/python-3.7.6-0/lib/python3.7/site-packages/tensorflow-2.1.0-py3.7-linux-x86_64.egg/tensorflow_core/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
        _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
      File "/dev/shm/python-3.7.6-0/lib/python3.7/imp.py", line 242, in load_module
        return load_dynamic(name, filename, file)
      File "/dev/shm/python-3.7.6-0/lib/python3.7/imp.py", line 342, in load_dynamic
        return _load(spec)
    ImportError: libnccl.so.2: cannot open shared object file: No such file or directory
---
 python-3.7.6-0.build.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 188369e..bd3b599 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -27,6 +27,7 @@ mkdir -p $PREFIX
 cat >$PREFIX/profile <<-EOF
 	. $CUDADIR/profile
 	PATH=$PREFIX/bin:\$PATH
+	export LD_LIBRARY_PATH=$PREFIX/lib\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH
 	PKG_CONFIG_PATH=$PREFIX/lib/pkgconfig\${PKG_CONFIG_PATH:+:\$PKG_CONFIG_PATH}
 	export PKG_CONFIG_PATH
 	if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi

From 961b8f5d53bf9f953c4a43fceb68d3b801f36420 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Fri, 27 Mar 2020 11:46:43 +0100
Subject: [PATCH 09/18] python-3.7.6: Add boost for pycuda

---
 python-3.7.6-0.build.sh | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index bd3b599..aa6ed56 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -241,6 +241,46 @@ pip3 install --prefix=$PREFIX libxml2-python3 # required by several bee packages
 pip3 install --prefix=$PREFIX scour           # https://github.molgen.mpg.de/mariux64/pkg-scripts/issues/98
 pip3 install --prefix=$PREFIX multiqc
 
+#boost for pycuda
+(
+	. ${PREFIX}/profile
+	BOOST_VERSION="1.72.0 1_72_0"
+	BOOST_SRC=https://dl.bintray.com/boostorg/release/$( echo $BOOST_VERSION | cut -d" " -f1 )/source/boost_$( echo $BOOST_VERSION | cut -d" " -f2 ).tar.gz
+	PKGCFLAGS="-O2 -fPIC"
+
+	cd $BUILDDIR
+	test -e boost_$( echo $BOOST_VERSION | cut -d" " -f2 ).tar.gz || wget $BOOST_SRC
+	test -d boost-$( echo $BOOST_VERSION | cut -d" " -f1 ) || mkdir boost-$( echo $BOOST_VERSION | cut -d" " -f1 ) && tar -xf boost_$( echo $BOOST_VERSION | cut -d" " -f2 ).tar.gz -C boost-$( echo $BOOST_VERSION | cut -d" " -f1 ) --strip-components=1
+
+	cd boost-$( echo $BOOST_VERSION | cut -d" " -f1 )
+	sed -e "/using python/ s|;|: ${PREFIX}/include/python${PYTHONVER}m ;|" \
+      -i bootstrap.sh
+
+	./bootstrap.sh \
+    --with-toolset=gcc \
+    --with-icu \
+    --with-python=$PREFIX/bin/python3 \
+    --with-libraries=python,thread || exit 1
+
+  ./b2 \
+    $NUMJOBS \
+    --layout=system \
+    --build-dir=build-python3 \
+    --prefix=$PREFIX \
+    --libdir=$PREFIX/lib \
+    --build-type=minimal \
+    toolset=gcc \
+    variant=release \
+    debug-symbols=off \
+    link=shared \
+    threading=multi \
+    runtime-link=shared \
+    python=$PYTHONVER \
+    cflags="$PKGCFLAGS" \
+    cxxflags="$PKGCFLAGS" \
+    install || exit 1
+)
+
 # try to load all packages, maybe we can see installation errors
 python3 -c 'help("modules")' > /dev/null
 

From 366b3314e4c1eb085e560659c2d1bf16aa0b83dd Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Fri, 27 Mar 2020 11:47:15 +0100
Subject: [PATCH 10/18] python-3.7.6: Add pycuda

---
 python-3.7.6-0.build.sh | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index aa6ed56..6eb3166 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -281,6 +281,33 @@ pip3 install --prefix=$PREFIX multiqc
     install || exit 1
 )
 
+#pycuda git version to get GL support
+(
+	PYCUDAVERS=2019.1.2
+
+	. ${PREFIX}/profile
+	cd $BUILDDIR
+	test -e pycuda-${PYCUDAVERS}.tar.gz || wget https://github.com/inducer/pycuda/archive/v${PYCUDAVERS}/pycuda-${PYCUDAVERS}.tar.gz
+	test -d pycuda-${PYCUDAVERS} || tar -xf pycuda-${PYCUDAVERS}.tar.gz
+	#test -d pycuda || git clone --recursive http://git.tiker.net/trees/pycuda.git
+
+	cd pycuda-${PYCUDAVERS}
+	test -e siteconf.py && rm siteconf.py
+	python3 configure.py \
+		--cuda-enable-gl \
+		--cuda-root=$CUDADIR \
+		--no-use-shipped-boost \
+		--boost-python-libname=boost_python37 \
+		--boost-inc-dir=$PREFIX/include \
+		--boost-lib-dir=$PREFIX/lib \
+		--cudadrv-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs' \
+		--cudart-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs' \
+		--curand-lib-dir='${CUDA_ROOT}/lib,${CUDA_ROOT}/lib/stubs'\
+		--ldflags=-L$PREFIX/lib
+
+	python3 setup.py install --prefix $PREFIX
+)
+
 # try to load all packages, maybe we can see installation errors
 python3 -c 'help("modules")' > /dev/null
 

From 3c5eade61483cb3765fff57ad0435eabea1d8b6c Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Thu, 26 Mar 2020 08:39:09 +0100
Subject: [PATCH 11/18] python-3.7.6: Change tmpdir

We are going to install Tensorflow into this package. The compilation of
Tendowflow produces huge amounts of data (335612 files, 35 GB) in
~/.cache/bazel.

Change BUILD_TMPDIR (which implies $HOME during the build) away from
/dev/shm to avoid running out of memory.
---
 python-3.7.6-0.build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 6eb3166..75fdd15 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -15,7 +15,7 @@ PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
 set -xe
 umask 022
 
-BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp
+BUILD_TMPDIR=/scratch/local2/$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

From 5e93e04d561fe4127982706ccad6466c3e071572 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Fri, 27 Mar 2020 12:04:20 +0100
Subject: [PATCH 12/18] python-3.7.6: Build hic2cool from source

The requireiments of hic2cool would downgrade a lot of packages, so
build it from source.
---
 python-3.7.6-0.build.sh | 36 +++++++++++++++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 75fdd15..38d6eb5 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -202,7 +202,6 @@ pip3 install --prefix=$PREFIX HTSeq
 pip3 install --prefix=$PREFIX keras
 pip3 install --prefix=$PREFIX MotifScan      # Alena 30.8.2018
 pip3 install --prefix=$PREFIX MAmotif
-pip3 install --prefix=$PREFIX hic2cool       # Helpdesk Robert Schoepflin 17.09.2018
 #pip3 install --prefix=$PREFIX hifive       # only python 2.7+
 pip3 install --prefix=$PREFIX snakemake
 pip3 install --prefix=$PREFIX virtualenv     # Donald
@@ -308,6 +307,41 @@ pip3 install --prefix=$PREFIX multiqc
 	python3 setup.py install --prefix $PREFIX
 )
 
+# hic2cool # Helpdesk Robert Schoepflin 17.09.2018
+# build from source to avoid downgrading other packages (scipy, numpy)
+(
+	HICVERS=0.8.0
+
+	. ${PREFIX}/profile
+	cd $BUILDDIR
+	test -e hic2cool-${HICVERS}.tar.gz || wget https://github.com/4dn-dcic/hic2cool/archive/${HICVERS}/hic2cool-${HICVERS}.tar.gz
+	test -d hic2cool-${HICVERS} || tar -xf hic2cool-${HICVERS}.tar.gz
+
+	cd hic2cool-${HICVERS}
+
+	if $( grep '==' requirements.txt >/dev/null ); then
+	patch -p1 <<'EOFHIC'
+diff --git a/requirements.txt b/requirements.txt
+index d7e701b..9d3a01c 100644
+--- a/requirements.txt
++++ b/requirements.txt
+@@ -1,5 +1,5 @@
+-h5py==2.8.0
+-pandas==0.24.2
+-numpy==1.16.3
+-scipy==1.2.1
+-cooler==0.8.5
++h5py
++pandas
++numpy
++scipy
++cooler
+EOFHIC
+fi
+	pip3 install -r requirements.txt --prefix ${PREFIX}
+	python3 setup.py install --prefix ${PREFIX}
+)
+
 # try to load all packages, maybe we can see installation errors
 python3 -c 'help("modules")' > /dev/null
 

From f95f7c14cd5a734e2fdd2f2ded1cad8b2e162556 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Thu, 26 Mar 2020 08:52:08 +0100
Subject: [PATCH 13/18] python-3.7.6: build tensorflow from source

---
 python-3.7.6-0.build.sh | 73 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 72 insertions(+), 1 deletion(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 38d6eb5..8b70123 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -212,7 +212,6 @@ pip3 install --prefix=$PREFIX louvain        # monocle3 prep for Helene
 pip3 install --prefix=$PREFIX selenium       # 19.7.19 Kreitler  -> https://webxray.org/
 pip3 install --prefix=$PREFIX cooltools      # Maria Valieva 17.7.2019
 pip3 install --prefix=$PREFIX gmpy           # From viper context (Helpdesk Laura Glaser 9.8.2019)
-pip3 install --prefix=$PREFIX tensorflow==2.0.1         # tensorflow-2.1.0 needs spezial libs and nightly version(2.2.0) dont
 pip3 install --prefix=$PREFIX torch
 pip3 install --prefix=$PREFIX torchvision
 pip3 install --prefix=$PREFIX plotly
@@ -342,6 +341,78 @@ fi
 	python3 setup.py install --prefix ${PREFIX}
 )
 
+#tensorflow
+(
+	TFVERSION=2.1.0
+	TFSRC=https://github.com/tensorflow/tensorflow/archive/v${TFVERSION}/tensorflow-${TFVERSION}.tar.gz
+
+
+	. ${PREFIX}/profile
+	. /pkg/bazel-0.28.1-0/profile
+	cd $BUILDDIR
+	test -e tensorflow-${TFVERSION}.tar.gz || wget $TFSRC
+	test -d tensorflow-${TFVERSION} || tar -xf tensorflow-${TFVERSION}.tar.gz
+
+	cd tensorflow-${TFVERSION}
+
+	#vars for config
+	export PYTHON_BIN_PATH=${PREFIX}/bin/python3
+	export USE_DEFAULT_PYTHON_LIB_PATH=1
+	export TF_NEED_JEMALLOC=1
+	export TF_NEED_KAFKA=0
+	export TF_NEED_OPENCL_SYCL=0
+	export TF_NEED_AWS=0
+	export TF_NEED_GCP=0
+	export TF_NEED_HDFS=0
+	export TF_NEED_S3=0
+	export TF_ENABLE_XLA=1
+	export TF_NEED_GDR=0
+	export TF_NEED_VERBS=0
+	export TF_NEED_OPENCL=0
+	export TF_NEED_MPI=0
+	export TF_NEED_TENSORRT=1
+	export TF_NEED_NGRAPH=0
+	export TF_NEED_IGNITE=0
+	export TF_NEED_ROCM=0
+	export TF_SET_ANDROID_WORKSPACE=0
+	export TF_DOWNLOAD_CLANG=0
+	export TF_NCCL_VERSION=2.5
+	export TF_IGNORE_MAX_BAZEL_VERSION=1
+	export NCCL_INSTALL_PATH=${CUDADIR}
+	export GCC_HOST_COMPILER_PATH=/usr/bin/gcc
+	export TF_CUDA_CLANG=0
+	export CLANG_CUDA_COMPILER_PATH=/usr/bin/clang
+	export TF_CUDA_PATHS=${CUDADIR},${CUDADIR}/extras/CUPTI,${CUDADIR}/nvvm
+	export TF_CUDA_VERSION=$(${CUDADIR}/bin/nvcc --version | sed -n 's/^.*release \(.*\),.*/\1/p')
+	export TF_CUDNN_VERSION=$(sed -n 's/^#define CUDNN_MAJOR\s*\(.*\).*/\1/p' ${CUDADIR}/include/cudnn.h)
+	export TF_CUDA_COMPUTE_CAPABILITIES=3.5,3.7,5.0,5.2,5.3,6.0,6.1,6.2,7.0,7.2,7.5
+	export CC_OPT_FLAGS="-march=nehalem"
+	export TF_NEED_CUDA=1
+
+	./configure
+	bazel build \
+		--cxxopt="-march=nehalem" \
+		--copt="-march=nehalem" \
+		//tensorflow:libtensorflow.so \
+		//tensorflow:libtensorflow_cc.so \
+		//tensorflow:install_headers \
+		//tensorflow/tools/pip_package:build_pip_package
+
+	test -d tensorflow-pip && rm -r tensorflow-pip
+	mkdir tensorflow-pip
+	./bazel-bin/tensorflow/tools/pip_package/build_pip_package --src ${BUILDDIR}/tensorflow-pip
+	cd ${BUILDDIR}
+	#remove symlinks into TMPDIR
+	test -e tensorflow-pip.tar && rm tensorflow-pip.tar
+	tar -chf tensorflow-pip.tar tensorflow-pip
+	test -d tensorflow-pip && rm -r tensorflow-pip
+
+	tar -xf tensorflow-pip.tar
+	cd ${BUILDDIR}/tensorflow-pip
+	python3 setup.py build
+	python3 setup.py install --prefix $PREFIX
+)
+
 # try to load all packages, maybe we can see installation errors
 python3 -c 'help("modules")' > /dev/null
 

From 39dc7168d7223c27ed6e4e9dca5ae0532a603042 Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Sat, 28 Mar 2020 13:28:51 +0100
Subject: [PATCH 14/18] python-3.7.6: Downgrade pyGenomeTracks

The latest version of pyGenomeTracks on PyPi (3.3) has a dependency on
hicmatrix>=12 which is not yet published. Request previous version.
---
 python-3.7.6-0.build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 8b70123..4713509 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -229,7 +229,7 @@ rm -rf ${PREFIX}/lib/python$PYTHONVER/site-packages/OpenGL/Tk
 
 # pip3 install --prefix=$PREFIX HiCExplorer  # Would be a nice to have, but it likes to downgrade too much, pick some cherries
 pip3 install --prefix=$PREFIX HiCMatrix
-pip3 install --prefix=$PREFIX pyGenomeTracks #downgrader cooler 0.8.7-> 0.8.5
+pip3 install --prefix=$PREFIX "pyGenomeTracks<3.3" # 3.3 depends on HiMatrix>=12 which is not yet available
 
 pip3 install --prefix=$PREFIX python-bioformats #downgrader matplotlib 3.2.0->3.1.1 docutils 0.16 -> 0.15.2
 

From 12a32bc59a89b1a844f61e5e54f33f22846ffc5f Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Sat, 28 Mar 2020 14:28:56 +0100
Subject: [PATCH 15/18] python-3.7.6: Use array for BOOST_VERSION

Store the variants of BOOST_VERSION in an array instead of in a space
seperated string to avoid parsing it over and over.
---
 python-3.7.6-0.build.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 4713509..78ea19a 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -242,15 +242,15 @@ pip3 install --prefix=$PREFIX multiqc
 #boost for pycuda
 (
 	. ${PREFIX}/profile
-	BOOST_VERSION="1.72.0 1_72_0"
-	BOOST_SRC=https://dl.bintray.com/boostorg/release/$( echo $BOOST_VERSION | cut -d" " -f1 )/source/boost_$( echo $BOOST_VERSION | cut -d" " -f2 ).tar.gz
+	BOOST_VERSION=(1.72.0 1_72_0)
+	BOOST_SRC=https://dl.bintray.com/boostorg/release/${BOOST_VERSION[0]}/source/boost_${BOOST_VERSION[1]}.tar.gz
 	PKGCFLAGS="-O2 -fPIC"
 
 	cd $BUILDDIR
-	test -e boost_$( echo $BOOST_VERSION | cut -d" " -f2 ).tar.gz || wget $BOOST_SRC
-	test -d boost-$( echo $BOOST_VERSION | cut -d" " -f1 ) || mkdir boost-$( echo $BOOST_VERSION | cut -d" " -f1 ) && tar -xf boost_$( echo $BOOST_VERSION | cut -d" " -f2 ).tar.gz -C boost-$( echo $BOOST_VERSION | cut -d" " -f1 ) --strip-components=1
+	test -e boost_${BOOST_VERSION[1]}.tar.gz || wget $BOOST_SRC
+	test -d boost-${BOOST_VERSION[0]} || mkdir boost-${BOOST_VERSION[0]} && tar -xf boost_${BOOST_VERSION[1]}.tar.gz -C boost-${BOOST_VERSION[0]} --strip-components=1
 
-	cd boost-$( echo $BOOST_VERSION | cut -d" " -f1 )
+	cd boost-${BOOST_VERSION[0]}
 	sed -e "/using python/ s|;|: ${PREFIX}/include/python${PYTHONVER}m ;|" \
       -i bootstrap.sh
 

From 3b780b3780b92b40d271d5f627a2f1d94885cd77 Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Sat, 28 Mar 2020 14:33:04 +0100
Subject: [PATCH 16/18] python-3.7.6: Use cached copy of boost download

The distribuition server seems to be broken at the moment:

    + wget https://dl.bintray.com/boostorg/release/1.72.0/source/boost_1_72_0.tar.gz
    --2020-03-28 13:02:47--  https://dl.bintray.com/boostorg/release/1.72.0/source/boost_1_72_0.tar.gz
    Resolving dl.bintray.com... 52.28.187.224, 52.29.129.139
    Connecting to dl.bintray.com|52.28.187.224|:443... connected.
    HTTP request sent, awaiting response... 403 Forbidden
    2020-03-28 13:02:47 ERROR 403: Forbidden.

Use cached copy.
---
 python-3.7.6-0.build.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 78ea19a..dabe6f0 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -247,7 +247,9 @@ pip3 install --prefix=$PREFIX multiqc
 	PKGCFLAGS="-O2 -fPIC"
 
 	cd $BUILDDIR
-	test -e boost_${BOOST_VERSION[1]}.tar.gz || wget $BOOST_SRC
+	# 28.03.2020: upstream server currently broken - use cached archive
+	#test -e boost_${BOOST_VERSION[1]}.tar.gz || wget $BOOST_SRC
+	test -e boost_${BOOST_VERSION[1]}.tar.gz || cp /src/mariux/beeroot/downloads/boost_${BOOST_VERSION[1]}.tar.gz .
 	test -d boost-${BOOST_VERSION[0]} || mkdir boost-${BOOST_VERSION[0]} && tar -xf boost_${BOOST_VERSION[1]}.tar.gz -C boost-${BOOST_VERSION[0]} --strip-components=1
 
 	cd boost-${BOOST_VERSION[0]}

From ad8038a3fd5db2701818f8a30c0d57b0890af50d Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Sun, 29 Mar 2020 15:12:07 +0200
Subject: [PATCH 17/18] Revert "python-3.7.6: Build hic2cool from source"

This reverts commit 5e93e04d561fe4127982706ccad6466c3e071572.

The requirements of hic2cool have been updated and we can fetch it with
pip again [1] [2]

[1]: https://github.com/4dn-dcic/hic2cool/issues/46
[2]: https://github.com/4dn-dcic/hic2cool/releases/tag/0.8.2
---
 python-3.7.6-0.build.sh | 36 +-----------------------------------
 1 file changed, 1 insertion(+), 35 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index dabe6f0..935c69f 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -202,6 +202,7 @@ pip3 install --prefix=$PREFIX HTSeq
 pip3 install --prefix=$PREFIX keras
 pip3 install --prefix=$PREFIX MotifScan      # Alena 30.8.2018
 pip3 install --prefix=$PREFIX MAmotif
+pip3 install --prefix=$PREFIX hic2cool       # Helpdesk Robert Schoepflin 17.09.2018
 #pip3 install --prefix=$PREFIX hifive       # only python 2.7+
 pip3 install --prefix=$PREFIX snakemake
 pip3 install --prefix=$PREFIX virtualenv     # Donald
@@ -308,41 +309,6 @@ pip3 install --prefix=$PREFIX multiqc
 	python3 setup.py install --prefix $PREFIX
 )
 
-# hic2cool # Helpdesk Robert Schoepflin 17.09.2018
-# build from source to avoid downgrading other packages (scipy, numpy)
-(
-	HICVERS=0.8.0
-
-	. ${PREFIX}/profile
-	cd $BUILDDIR
-	test -e hic2cool-${HICVERS}.tar.gz || wget https://github.com/4dn-dcic/hic2cool/archive/${HICVERS}/hic2cool-${HICVERS}.tar.gz
-	test -d hic2cool-${HICVERS} || tar -xf hic2cool-${HICVERS}.tar.gz
-
-	cd hic2cool-${HICVERS}
-
-	if $( grep '==' requirements.txt >/dev/null ); then
-	patch -p1 <<'EOFHIC'
-diff --git a/requirements.txt b/requirements.txt
-index d7e701b..9d3a01c 100644
---- a/requirements.txt
-+++ b/requirements.txt
-@@ -1,5 +1,5 @@
--h5py==2.8.0
--pandas==0.24.2
--numpy==1.16.3
--scipy==1.2.1
--cooler==0.8.5
-+h5py
-+pandas
-+numpy
-+scipy
-+cooler
-EOFHIC
-fi
-	pip3 install -r requirements.txt --prefix ${PREFIX}
-	python3 setup.py install --prefix ${PREFIX}
-)
-
 #tensorflow
 (
 	TFVERSION=2.1.0

From a4dcb65f83ed6ea76325f5af6c3ad1f363c1fbbe Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Mon, 30 Mar 2020 17:59:16 +0200
Subject: [PATCH 18/18] Update python-3.7.6 to python-3.7.7

Create bee file with

    mv python-3.7.6.build.sh python-3.7.7.build.sh

and update version.
---
 python-3.7.6-0.build.sh => python-3.7.7-0.build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename python-3.7.6-0.build.sh => python-3.7.7-0.build.sh (99%)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.7-0.build.sh
similarity index 99%
rename from python-3.7.6-0.build.sh
rename to python-3.7.7-0.build.sh
index 935c69f..52b1691 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.7-0.build.sh
@@ -1,7 +1,7 @@
 #! /bin/bash
 
 PKG=python
-VERSION=3.7.6
+VERSION=3.7.7
 BUILD=0
 PYTHONVER=${VERSION%.*}