snakemake: Build a separate version 7

Snakemake is part of the packaged python, but since the larger python
upgrade is still pending, install the tool as snakemake7.

snakemake-7.1.1-0.build.sh

@@ -0,0 +1,69 @@
+#! /bin/bash
+
+# COOKIE=$(mcookie|cut -c-8); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 0.3; exec bash /dev/shm/runme-$COOKIE.sh
+# TESTING=1
+
+PKG=snakemake
+VERSION=7.1.1
+
+PYTHONVERSION=3.9.10
+BUILD=0
+PYTHONVER=${PYTHONVERSION%.*}
+
+PREFIX=/pkg/$PKG-$VERSION-$BUILD
+if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi
+
+PATH=/bin:/usr/bin:/usr/sbin:/usr/local/bin
+
+set -xe
+umask 022
+
+BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.$USER.build.tmp
+
+test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR )
+mkdir -p $BUILD_TMPDIR/home/.cache/pip
+mkdir -p $BUILD_TMPDIR/home/.local
+export TMPDIR=$BUILD_TMPDIR
+export HOME=$BUILD_TMPDIR/home
+
+exec </dev/null
+
+mkdir -p $PREFIX
+cat >$PREFIX/profile <<-EOF
+	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
+EOF
+. $PREFIX/profile
+
+NPROC=$(( $(nproc) * 4 / 5 + 1 ))
+export MAKEFLAGS="-j $NPROC"
+
+BUILDDIR=$PREFIX/build
+
+mkdir -p $BUILDDIR
+cd $BUILDDIR
+
+# orig: https://www.python.org/ftp/python/3.9.10/Python-3.9.10.tgz
+BEEHIVE=https://beehive.molgen.mpg.de/1440acb71471e2394befdb30b1a958d1/Python-3.9.10.tgz
+test -e Python-$PYTHONVERSION.tgz || wget -nv $BEEHIVE
+test -d Python-$PYTHONVERSION || tar -xf Python-$PYTHONVERSION.tgz
+cd Python-$PYTHONVERSION
+
+LDFLAGS="-Wl,-rpath=$PREFIX/lib" \
+./configure \
+        --prefix=$PREFIX \
+        --enable-shared
+
+make -j $NPROC
+make install
+
+# it might come to happen that something down the line may just call 'python', defuse ...
+test -e $PREFIX/bin/python || ln -s python3 $PREFIX/bin/python
+
+python3 -m ensurepip
+pip3 install --prefix=$PREFIX -I pip
+pip3 install --prefix=$PREFIX snakemake==$VERSION
+