From 6ceff5e7684573b8bce28fe5ec18a02494076a8d Mon Sep 17 00:00:00 2001
From: brobr
Date: Fri, 15 Oct 2021 12:33:57 +0100
Subject: academic/pysam: Updated for version 0.17.0

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/pysam/pysam.SlackBuild | 23 ++++++-----------------
 academic/pysam/pysam.info       |  8 ++++----
 2 files changed, 10 insertions(+), 21 deletions(-)

(limited to 'academic/pysam')

diff --git a/academic/pysam/pysam.SlackBuild b/academic/pysam/pysam.SlackBuild
index 1daa466668..55994c9694 100644
--- a/academic/pysam/pysam.SlackBuild
+++ b/academic/pysam/pysam.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for pysam
 
-# Copyright 2017-2020 Rob van Nues
+# Copyright 2017-2021 Rob van Nues
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -22,19 +22,14 @@
 #  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-
 cd $(dirname $0) ; CWD=$(pwd)
 
 PRGNAM=pysam
-VERSION=${VERSION:-0.16.0.1}
+VERSION=${VERSION:-0.17.0}
 BUILD=${BUILD:-3}
 TAG=${TAG:-_SBo}
 PKGTYPE=${PKGTYPE:-tgz}
 
-#set which python version to install it for
-PYTHON2=false
-PYTHON3=true
-
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
     i?86) ARCH=i586 ;;
@@ -85,21 +80,15 @@ find -L . \
  \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
   -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-### pysam linked to htslib-1.10; SBo-htslib is at 1.11:
+### pysam linked to htslib-1.13; SBo-htslib is at 1.13:
 ##use system htslib:
-#export HTSLIB_LIBRARY_DIR=/usr/lib$LIBDIRSUFFIX
-#export HTSLIB_INCLUDE_DIR=/usr/include
+export HTSLIB_LIBRARY_DIR=/usr/lib$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
+python3 setup.py install --root=$PKG
 
 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
diff --git a/academic/pysam/pysam.info b/academic/pysam/pysam.info
index 1b2eddc4da..f49bd25d6c 100644
--- a/academic/pysam/pysam.info
+++ b/academic/pysam/pysam.info
@@ -1,10 +1,10 @@
 PRGNAM="pysam"
-VERSION="0.16.0.1"
+VERSION="0.17.0"
 HOMEPAGE="https://github.com/pysam-developers/pysam"
-DOWNLOAD="https://pypi.python.org/packages/source/p/pysam/pysam-0.16.0.1.tar.gz"
-MD5SUM="5b4b73431f2511727f4fef43a67b392e"
+DOWNLOAD="https://pypi.python.org/packages/source/p/pysam/pysam-0.17.0.tar.gz"
+MD5SUM="cddcf9bad79158fb2e2f9859c5188206"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
-REQUIRES=""
+REQUIRES="htslib"
 MAINTAINER="Rob van Nues"
 EMAIL="sborg63@disroot.org"
-- 
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