From 6cd83d27853d35ec172b3445d0b094a590b3762c Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
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 </dev/null
+
+mkdir -p $PREFIX
+cat >$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 <buczek@molgen.mpg.de>
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-$BUILD ; fi
From 6b2da52279f111c48ae50ef840454dce170cfece Mon Sep 17 00:00:00 2001
From: Donald Buczek <buczek@molgen.mpg.de>
Date: Tue, 30 Apr 2019 16:27:50 +0200
Subject: [PATCH 3/5] python-3.7.3-0: Update to lastest TEMPLATE
---
python-3.7.3-0.build.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/python-3.7.3-0.build.sh b/python-3.7.3-0.build.sh
index d6e463e..3f061e9 100755
--- a/python-3.7.3-0.build.sh
+++ b/python-3.7.3-0.build.sh
@@ -10,7 +10,7 @@ set -xe
umask 022
BUILD_TMPDIR=/dev/shm/$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 <buczek@molgen.mpg.de>
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 <buczek@molgen.mpg.de>
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