diff options
Diffstat (limited to 'academic/pysam/pysam.SlackBuild')
| -rw-r--r-- | academic/pysam/pysam.SlackBuild | 30 |
1 files changed, 25 insertions, 5 deletions
diff --git a/academic/pysam/pysam.SlackBuild b/academic/pysam/pysam.SlackBuild index c2ff916cc9..dcbc06e1a6 100644 --- a/academic/pysam/pysam.SlackBuild +++ b/academic/pysam/pysam.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for pysam -# Copyright 2017 Rob van Nues +# Copyright 2017-2020 Rob van Nues # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,10 +24,14 @@ PRGNAM=pysam -VERSION=${VERSION:-0.15.2} -BUILD=${BUILD:-1} +VERSION=${VERSION:-0.16.0.1} +BUILD=${BUILD:-3} TAG=${TAG:-_SBo} +#set which python version to install it for +PYTHON2=false +PYTHON3=true + if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -64,13 +68,28 @@ rm -rf $PRGNAM-$VERSION tar xvf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . + find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + \( -perm 777 -o -perm 775 -o -perm 751 -o -perm 750 -o -perm 711 -o -perm 555 \ -o -perm 511 \) -exec chmod 755 {} \; -o \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -python setup.py install --root=$PKG +### pysam linked to htslib-1.10; SBo-htslib is at 1.11: +##use system htslib: +#export HTSLIB_LIBRARY_DIR=/usr/lib$LIBDIRSUFFIX +#export HTSLIB_INCLUDE_DIR=/usr/include + +#the source does not allow 'read' to 'other', which could cause a problem on reloading a Jupyter-notebook +chmod 644 pysam.egg-info/* + + +if $PYTHON2; then + python setup.py install --root=$PKG +fi +if $PYTHON3; then + python3 setup.py install --root=$PKG +fi find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true @@ -81,6 +100,7 @@ cp -a \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc |