From 6cd83d27853d35ec172b3445d0b094a590b3762c Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Tue, 30 Apr 2019 16:25:47 +0200 Subject: [PATCH 1/5] Add python-3.7.3-0 Created with cp python-3.7.1-2.build.sh python-3.7.3-0.build.sh --- python-3.7.3-0.build.sh | 124 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 124 insertions(+) create mode 100755 python-3.7.3-0.build.sh diff --git a/python-3.7.3-0.build.sh b/python-3.7.3-0.build.sh new file mode 100755 index 0000000..f739e04 --- /dev/null +++ b/python-3.7.3-0.build.sh @@ -0,0 +1,124 @@ +#! /bin/bash + +PKG=python +VERSION=3.7.1 +BUILD=2 +PREFIX=/pkg/$PKG-$VERSION-$BUILD +if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi + +set -xe +umask 022 + +BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp +test -d $BUILD_TMPDIR && rm -rf $BUILD_TMPDIR +mkdir -p $BUILD_TMPDIR/home +export TMPDIR=$BUILD_TMPDIR +export HOME=$BUILD_TMPDIR/home + +exec $PREFIX/profile <<-EOF + PATH=$PREFIX/bin:\$PATH + if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:\$LD_LIBRARY_PATH} ; fi +EOF +. $PREFIX/profile + +export MAKEFLAGS="-j $(nproc)" + +BUILDDIR=$PREFIX/build + +mkdir -p $BUILDDIR +cd $BUILDDIR + +test -e Python-$VERSION.tar.xz || wget https://www.python.org/ftp/python/$VERSION/Python-$VERSION.tar.xz +test -d Python-$VERSION || tar xvf Python-$VERSION.tar.xz +cd Python-$VERSION + +LDFLAGS="-Wl,-rpath=$PREFIX/lib" \ +./configure \ + --prefix=$PREFIX \ + --enable-shared + +make -j $(nproc) +# make test || true # 'test_socket' seems to run for ever +make install + +( # sip: tool to create Python bindings for C and C++ libraries. + cd $PREFIX/build + SIP_VERSION=4.19.13 + SIP_SRC=https://sourceforge.net/projects/pyqt/files/sip/sip-$SIP_VERSION/sip-$SIP_VERSION.tar.gz + test -e sip-$SIP_VERSION.tar.gz || wget $SIP_SRC + test -d sip-$SIP_VERSION || tar -xf sip-$SIP_VERSION.tar.gz + + PYTHONVER=$( echo $VERSION | cut -f 1-2 -d. ) + cd sip-$SIP_VERSION + + python3 configure.py \ + -b $PREFIX/bin \ + -d $PREFIX/lib/python$PYTHONVER/site-packages \ + -e $PREFIX/include/python${PYTHONVER}m \ + -v $PREFIX/share/sip + + mkdir -p $PREFIX/share/sip + make; make install +) + +python3 -m ensurepip +pip3 install -I pip + +pip3 install ipython[all] +pip3 install SciPy NumPy Matplotlib pandas SymPy nose statsmodels + +pip3 install Cython + +pip3 install pysam +pip3 install seaborn +pip3 install scikit-learn +# pip3 install metaseq # fails (Latest commit fa875d1 on Jan 10, 2017) +pip3 install Mako +pip3 install meson + +# Helpdesk 01/24/18 16:19, Sabrina Krakau +pip3 install cutadapt + +#Helpdesk 03/26/18 14:19, Virginie Stanisla +pip3 install pygobject + +pip3 install python-bioformats +pip3 install umi-tools +pip3 install sphinx +pip3 install recommonmark +pip3 install fastcluster +pip3 install pydot +pip3 install pygraphviz +pip3 install deeptools +pip3 install HTSeq +pip3 install keras + +# Alena 30.8.2018 +pip3 install MotifScan +pip3 install MAmotif + +pip3 install hic2cool # helpdesk robert schoepflin 17.09.2018 +# pip3 install hifive # only 2.7+ + +# snakemake likes to have this one, but datrie isn't 3.7 aware ... +# luckily a fix is available (https://github.com/pytries/datrie/issues/52) +( + DATRIE_PY_VERSION=0.7.1 + DATRIE_PY_SRC=https://github.com/pytries/datrie/archive/$DATRIE_PY_VERSION.tar.gz + cd $PREFIX/build + test -e $DATRIE_PY_VERSION.tar.gz || wget $DATRIE_PY_SRC + test -d datrie-$DATRIE_PY_VERSION || tar -xf $DATRIE_PY_VERSION.tar.gz + + cd datrie-$DATRIE_PY_VERSION + ./update_c.sh + python3.7 setup.py build + python3.7 setup.py install +) +pip3 install snakemake +pip3 install virtualenv # Donald +pip3 install odfpy # Donald + +exit From 80bf1e9150c6f8c1807657089698224bf4d66c9c Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Tue, 30 Apr 2019 16:27:12 +0200 Subject: [PATCH 2/5] python-3.7.3-0: Update version and build number --- python-3.7.3-0.build.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python-3.7.3-0.build.sh b/python-3.7.3-0.build.sh index f739e04..d6e463e 100755 --- a/python-3.7.3-0.build.sh +++ b/python-3.7.3-0.build.sh @@ -1,8 +1,8 @@ #! /bin/bash PKG=python -VERSION=3.7.1 -BUILD=2 +VERSION=3.7.3 +BUILD=0 PREFIX=/pkg/$PKG-$VERSION-$BUILD if [ -n "$TESTING" ]; then PREFIX=/dev/shm/$PKG-$VERSION-$BUILD ; fi From 6b2da52279f111c48ae50ef840454dce170cfece Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Tue, 30 Apr 2019 16:27:50 +0200 Subject: [PATCH 3/5] python-3.7.3-0: Update to lastest TEMPLATE --- python-3.7.3-0.build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python-3.7.3-0.build.sh b/python-3.7.3-0.build.sh index d6e463e..3f061e9 100755 --- a/python-3.7.3-0.build.sh +++ b/python-3.7.3-0.build.sh @@ -10,7 +10,7 @@ set -xe umask 022 BUILD_TMPDIR=/dev/shm/$PKG-$VERSION-$BUILD.build.tmp -test -d $BUILD_TMPDIR && rm -rf $BUILD_TMPDIR +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 From 9aa0c8cd9f2dee96482e1924a1b270c876f30b47 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Tue, 30 Apr 2019 16:28:32 +0200 Subject: [PATCH 4/5] python-3.7.3-0: Add blink1 Readd blink1 which was accidentally removed by b5e87b4d7b474195546cc35a1f237344c097ec2e ("python: Add version 3.7.1") --- python-3.7.3-0.build.sh | 3 +++ 1 file changed, 3 insertions(+) diff --git a/python-3.7.3-0.build.sh b/python-3.7.3-0.build.sh index 3f061e9..fe1020a 100755 --- a/python-3.7.3-0.build.sh +++ b/python-3.7.3-0.build.sh @@ -85,6 +85,9 @@ pip3 install cutadapt #Helpdesk 03/26/18 14:19, Virginie Stanisla pip3 install pygobject +# Blink1-lib 07/04/18 12:00, Niclas Hofmann +pip3 install blink1 + pip3 install python-bioformats pip3 install umi-tools pip3 install sphinx From 2e2aefea07f24257d88045c7c34a0b1a889c4683 Mon Sep 17 00:00:00 2001 From: Donald Buczek Date: Tue, 30 Apr 2019 16:53:26 +0200 Subject: [PATCH 5/5] python-3.7: Add Dumper Add Dumper as requested by @thomas. --- python-3.7.3-0.build.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/python-3.7.3-0.build.sh b/python-3.7.3-0.build.sh index fe1020a..635cc2a 100755 --- a/python-3.7.3-0.build.sh +++ b/python-3.7.3-0.build.sh @@ -123,5 +123,6 @@ pip3 install hic2cool # helpdesk robert schoepflin 17.09.2018 pip3 install snakemake pip3 install virtualenv # Donald pip3 install odfpy # Donald +pip3 install Dumper # Thomas exit