Add/update python 3.7.6

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
@@ -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
@@ -175,7 +175,7 @@ make install
 python3 -m ensurepip
 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
 # clean up some dirt that statsmodels placed also into $PREFIX
@@ -217,7 +217,6 @@ pip3 install --prefix=$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=$PREFIX plotly
@@ -231,18 +230,19 @@ pip3 install --prefix=$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 --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
 (
@@ -265,24 +265,6 @@ 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 \
     $NUMJOBS \
     --layout=system \
@@ -304,25 +286,135 @@ pip3 install --prefix=$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 \
-    --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