From bb877fc5073c153a6db3cf7c31697b55eff53657 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Wed, 11 Mar 2020 13:51:44 +0100
Subject: [PATCH 01/13] tensorflow build from source

---
 python-3.7.6-0.build.sh | 63 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 62 insertions(+), 1 deletion(-)
 mode change 100644 => 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
old mode 100644
new mode 100755
index 186ee89..6532b49
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -217,7 +217,6 @@ 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
@@ -324,6 +323,68 @@ pip3 install --prefix=$PREFIX scour           # https://github.molgen.mpg.de/mar
 
 	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=native"
+	export TF_NEED_CUDA=1
+
+	./configure
+	bazel build \
+		//tensorflow:libtensorflow.so \
+		//tensorflow:libtensorflow_cc.so \
+		//tensorflow:install_headers \
+		//tensorflow/tools/pip_package:build_pip_package
+
+		mkdir tf-src
+		./bazel-bin/tensorflow/tools/pip_package/build_pip_package -src ./tf-src
+		cd tf-src
+		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 65c3b732793f553e822ec6d025cbebd7128fec56 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Wed, 11 Mar 2020 13:52:37 +0100
Subject: [PATCH 02/13] remove is not need, the install part is enough

---
 python-3.7.6-0.build.sh | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 6532b49..550eca0 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -264,24 +264,6 @@ pip3 install --prefix=$PREFIX scour           # https://github.molgen.mpg.de/mar
     --with-python=$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 \

From 422537693747c443602b8bef55d7d2ce88c24625 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Wed, 11 Mar 2020 14:12:14 +0100
Subject: [PATCH 03/13] pucuda change lib path

---
 python-3.7.6-0.build.sh | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 550eca0..5b2f1c5 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -285,12 +285,16 @@ pip3 install --prefix=$PREFIX scour           # https://github.molgen.mpg.de/mar
 
 #pycuda git version to get GL support
 (
+	PYCUDAVERS=2019.1.2
+
 	. ${PREFIX}/profile
 	cd $BUILDDIR
-	test -d pycuda || git clone --recursive http://git.tiker.net/trees/pycuda.git
+	test -e pycuda-${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
-	git clean -dffx
+	cd pycuda-${PYCUDAVERS}
+	test -e siteconf.py && rm siteconf.py
 	python3 configure.py \
     --cuda-enable-gl \
     --cuda-root=$CUDADIR \
@@ -298,9 +302,9 @@ pip3 install --prefix=$PREFIX scour           # https://github.molgen.mpg.de/mar
     --boost-python-libname=boost_python37 \
     --boost-inc-dir=$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,${CUDA_ROOT}/lib64/stubs'\
+    --cudadrv-lib-dir='${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

From 7a1b9080b83b4b242213ea58bd89b6653d7ea542 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Wed, 11 Mar 2020 14:13:09 +0100
Subject: [PATCH 04/13] bazel needs a lot of space

---
 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 5b2f1c5..1dfb51b 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -18,7 +18,7 @@ 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 08775651422a36458c39684a0de850bc5d5dc7f6 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Wed, 11 Mar 2020 14:13:27 +0100
Subject: [PATCH 05/13] latest cudaversion

---
 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 1dfb51b..f69e5e4 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -8,7 +8,7 @@ VERSION=3.7.6
 BUILD=0
 PYTHONVER=${VERSION%.*}
 
-CUDADIR=/pkg/cuda-10.1.105-0
+CUDADIR=/pkg/cuda-10.2.89-1
 
 PREFIX=/pkg/$PKG-$VERSION-$BUILD
 if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi

From 4dd95b6140e44dab263b0af0f5cc89e4b9974f70 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Wed, 11 Mar 2020 14:14:59 +0100
Subject: [PATCH 06/13] wish from Robert Schoepflin

---
 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 f69e5e4..b5d0575 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -242,6 +242,7 @@ 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
 
 #boost for pycuda
 (

From 9baa7f534da7e758636167953a18332bc214cdcf Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Wed, 11 Mar 2020 14:16:18 +0100
Subject: [PATCH 07/13] build hic2cool from github

---
 python-3.7.6-0.build.sh | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index b5d0575..6b91ada 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -311,6 +311,37 @@ pip3 install --prefix=$PREFIX multiqc
 	python3 setup.py install --prefix $PREFIX
 )
 
+# hic2cool from to stop downgrading python packages
+(
+	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}
+	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
+	pip3 install -r requirements.txt --prefix ${PREFIX}
+	python3 setup.py install --prefix ${PREFIX}
+)
+
 #tensorflow
 (
 	TFVERSION=2.1.0

From 6d5f7684e5a11799646f0dd2a246e1ac75970494 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Wed, 11 Mar 2020 14:34:36 +0100
Subject: [PATCH 08/13] tensorflow: make sure tf use the right arch flags

---
 python-3.7.6-0.build.sh | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 6b91ada..08ef735 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -386,19 +386,21 @@ EOFHIC
 	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=native"
+	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
 
 		mkdir tf-src
-		./bazel-bin/tensorflow/tools/pip_package/build_pip_package -src ./tf-src
-		cd tf-src
+		./bazel-bin/tensorflow/tools/pip_package/build_pip_package -src ${BUILDDIR}/tensorflow-pip
+		cd ${BUILDDIR}/tensorflow-pip
 		python3 setup.py build
 		python3 setup.py install -- prefix $PREFIX
 

From 88aba6841982a50acb5fa9568e922f554e703ee8 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Wed, 11 Mar 2020 14:39:39 +0100
Subject: [PATCH 09/13] no idea

---
 python-3.7.6-0.build.sh | 413 +---------------------------------------
 1 file changed, 2 insertions(+), 411 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 08ef735..6b47346 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -1,411 +1,2 @@
-#! /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-10.2.89-1
-
-PREFIX=/pkg/$PKG-$VERSION-$BUILD
-if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
-
-PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
-
-set -xe
-umask 022
-
-BUILD_TMPDIR=/scratch/local2/$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
-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 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
-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
-)
-
-#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
-)
-
-# hic2cool from to stop downgrading python packages
-(
-	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}
-	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
-	pip3 install -r requirements.txt --prefix ${PREFIX}
-	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
-
-		mkdir tf-src
-		./bazel-bin/tensorflow/tools/pip_package/build_pip_package -src ${BUILDDIR}/tensorflow-pip
-		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
-
-exit
+sudo -u build script -q -e -c "./python-3.7.6-0.build.sh" /package/pkg/python-3.7.6-0/python-3.7.6-0.build.log
+bash: ./python-3.7.6-0.build.sh: Text file busy

From 9526a67a23620d9595976e7439458471f63a752d Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Thu, 6 Feb 2020 11:37:50 +0100
Subject: [PATCH 10/13] Update Python to version 3.7.6

---
 python-3.7.6-0.build.sh | 331 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 329 insertions(+), 2 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 6b47346..5ba4040 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -1,2 +1,329 @@
-sudo -u build script -q -e -c "./python-3.7.6-0.build.sh" /package/pkg/python-3.7.6-0/python-3.7.6-0.build.log
-bash: ./python-3.7.6-0.build.sh: Text file busy
+#! /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 -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 Would be a nice to have, but it likes to downgrade too much, pick some cherries
+#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 tensorflow==2.0.1         # tensorflow-2.1.0 tensorflow-gpu-2.0.1 downgrade dependencies from eachothers
+pip3 install tensorflow-gpu==2.0.1
+pip3 install torch
+pip3 install torchvision
+pip3 install plotly
+pip3 install pyOpenCL
+pip3 install pyopengl
+pip3 install docopt
+pip3 install dbus-python
+pip3 install distro
+pip3 install notify
+pip3 install ply
+pip3 install threadpoolctl
+
+
+# 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 jupyterlab-git
+. /pkg/node-12.4.0-0/profile
+${PREFIX}/bin/jupyter-labextension install @jupyterlab/github
+
+#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 cea7a5181a9ac988b5bb8ebf1e8fba3290cd060e Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Tue, 25 Feb 2020 09:16:48 +0100
Subject: [PATCH 11/13] python-3.7.6: add prefix on pip

pip default is now userdir
---
 python-3.7.6-0.build.sh | 123 ++++++++++++++++++++--------------------
 1 file changed, 62 insertions(+), 61 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 5ba4040..d4ede28 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -173,73 +173,74 @@ 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 Would be a nice to have, but it likes to downgrade too much, pick some cherries
-#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 tensorflow==2.0.1         # tensorflow-2.1.0 tensorflow-gpu-2.0.1 downgrade dependencies from eachothers
-pip3 install tensorflow-gpu==2.0.1
-pip3 install torch
-pip3 install torchvision
-pip3 install plotly
-pip3 install pyOpenCL
-pip3 install pyopengl
-pip3 install docopt
-pip3 install dbus-python
-pip3 install distro
-pip3 install notify
-pip3 install ply
-pip3 install threadpoolctl
-
-
-# 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 jupyterlab-git
+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
 . /pkg/node-12.4.0-0/profile
 ${PREFIX}/bin/jupyter-labextension install @jupyterlab/github
 

From 9733203166b6ff5b6b3a375bbbf99f158417a024 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Thu, 6 Feb 2020 11:37:50 +0100
Subject: [PATCH 12/13] Update Python to version 3.7.6

---
 python-3.7.6-0.build.sh | 69 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index d4ede28..0ebfeb6 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -173,15 +173,24 @@ make install
 )
 
 python3 -m ensurepip
+<<<<<<< HEAD
 pip3 install --prefix=$PREFIX -I pip
 
 pip3 install --prefix=$PREFIX ipython[all]
 
 pip3 install --prefix=$PREFIX SciPy NumPy Matplotlib pandas SymPy nose statsmodels
+=======
+pip3 install -I pip
+
+pip3 install ipython[all]
+
+pip3 install SciPy NumPy Matplotlib pandas SymPy nose statsmodels
+>>>>>>> Update Python to version 3.7.6
 # clean up some dirt that statsmodels placed also into $PREFIX
 rm -vf $PREFIX/LICENSE.txt
 rm -vf $PREFIX/setup.cfg
 
+<<<<<<< HEAD
 pip3 install --prefix=$PREFIX Cython
 
 pip3 install --prefix=$PREFIX pysam
@@ -241,6 +250,66 @@ pip3 install --prefix=$PREFIX python-bioformats
 
 pip3 install --prefix=$PREFIX jupyterlab      # request Peter Arndt
 pip3 install --prefix=$PREFIX jupyterlab-git
+=======
+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 Would be a nice to have, but it likes to downgrade too much, pick some cherries
+#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 tensorflow==2.0.1         # tensorflow-2.1.0 tensorflow-gpu-2.0.1 downgrade dependencies from eachothers
+pip3 install tensorflow-gpu==2.0.1
+pip3 install torch
+pip3 install torchvision
+pip3 install plotly
+pip3 install pyOpenCL
+pip3 install pyopengl
+pip3 install docopt
+pip3 install dbus-python
+pip3 install distro
+pip3 install notify
+pip3 install ply
+pip3 install threadpoolctl
+
+
+# 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 jupyterlab-git
+>>>>>>> Update Python to version 3.7.6
 . /pkg/node-12.4.0-0/profile
 ${PREFIX}/bin/jupyter-labextension install @jupyterlab/github
 

From 572c519cecb49ae1c1c1bf66dee016828a7187e5 Mon Sep 17 00:00:00 2001
From: david <schrader@molgen.mpg.de>
Date: Tue, 24 Mar 2020 08:47:57 +0100
Subject: [PATCH 13/13] Python-3.7.6: fix typo

---
 python-3.7.6-0.build.sh | 243 ++++++++++++++++++++++------------------
 1 file changed, 133 insertions(+), 110 deletions(-)

diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh
index 0ebfeb6..ed71f94 100755
--- a/python-3.7.6-0.build.sh
+++ b/python-3.7.6-0.build.sh
@@ -1,6 +1,6 @@
 #! /bin/bash
 
-#COOKIE=$(mcookie); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 1; exec bash /dev/shm/runme-$COOKIE.sh $1
+COOKIE=$(mcookie); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 1; exec bash /dev/shm/runme-$COOKIE.sh $1
 
 
 PKG=python
@@ -8,7 +8,7 @@ VERSION=3.7.6
 BUILD=0
 PYTHONVER=${VERSION%.*}
 
-CUDADIR=/pkg/cuda-10.1.105-0
+CUDADIR=/pkg/cuda-10.2.89-1
 
 PREFIX=/pkg/$PKG-$VERSION-$BUILD
 if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi
@@ -18,7 +18,7 @@ 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
@@ -173,24 +173,15 @@ make install
 )
 
 python3 -m ensurepip
-<<<<<<< HEAD
 pip3 install --prefix=$PREFIX -I pip
 
-pip3 install --prefix=$PREFIX ipython[all]
+pip3 install --upgrade --prefix=$PREFIX ipython[all]
 
 pip3 install --prefix=$PREFIX SciPy NumPy Matplotlib pandas SymPy nose statsmodels
-=======
-pip3 install -I pip
-
-pip3 install ipython[all]
-
-pip3 install SciPy NumPy Matplotlib pandas SymPy nose statsmodels
->>>>>>> Update Python to version 3.7.6
 # clean up some dirt that statsmodels placed also into $PREFIX
 rm -vf $PREFIX/LICENSE.txt
 rm -vf $PREFIX/setup.cfg
 
-<<<<<<< HEAD
 pip3 install --prefix=$PREFIX Cython
 
 pip3 install --prefix=$PREFIX pysam
@@ -226,7 +217,6 @@ pip3 install --prefix=$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=$PREFIX plotly
@@ -240,78 +230,19 @@ pip3 install --prefix=$PREFIX threadpoolctl
 
 pip3 install --prefix=$PREFIX pyopengl
 rm -rf ${PREFIX}/lib/python$PYTHONVER/site-packages/OpenGL/Tk
-# create error, so remove it
+# 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
-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
-=======
-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 Would be a nice to have, but it likes to downgrade too much, pick some cherries
-#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 tensorflow==2.0.1         # tensorflow-2.1.0 tensorflow-gpu-2.0.1 downgrade dependencies from eachothers
-pip3 install tensorflow-gpu==2.0.1
-pip3 install torch
-pip3 install torchvision
-pip3 install plotly
-pip3 install pyOpenCL
-pip3 install pyopengl
-pip3 install docopt
-pip3 install dbus-python
-pip3 install distro
-pip3 install notify
-pip3 install ply
-pip3 install threadpoolctl
-
-
-# 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 jupyterlab-git
->>>>>>> Update Python to version 3.7.6
-. /pkg/node-12.4.0-0/profile
-${PREFIX}/bin/jupyter-labextension install @jupyterlab/github
+pip3 install --prefix=$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
 
 #boost for pycuda
 (
@@ -334,24 +265,6 @@ ${PREFIX}/bin/jupyter-labextension install @jupyterlab/github
     --with-python=$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 \
@@ -373,26 +286,136 @@ ${PREFIX}/bin/jupyter-labextension install @jupyterlab/github
 
 #pycuda git version to get GL support
 (
+	PYCUDAVERS=2019.1.2
+
 	. ${PREFIX}/profile
 	cd $BUILDDIR
-	test -d pycuda || git clone --recursive http://git.tiker.net/trees/pycuda.git
+	test -e pycuda-${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
-	git clean -dffx
+	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='${CUDA_ROOT}/lib64,${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$PREFIX/lib
+  	--cuda-enable-gl \
+  	--cuda-root=$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
 )
+
+# hic2cool from source to stop downgrading python packages
+(
+	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 ${PREFIX}
+)
+
+#tensorflow
+(
+	TFVERSION=2.1.0
+	TFSRC=https://github.com/tensorflow/tensorflow/archive/v${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 -rf 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 -rf 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