academic/samtools: Updated for version 1.10.

Signed-off-by: Robby Workman <rworkman@slackbuilds.org>

1 files changed, 17 insertions, 19 deletions

diff --git a/academic/samtools/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild
index daa7e87daf..4a7efb30d8 100644
--- a/academic/samtools/samtools.SlackBuild
+++ b/academic/samtools/samtools.SlackBuild
@@ -3,7 +3,7 @@
 # Slackware build script for samtools
 
 # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com
-# Copyright 2017-2018 Rob van Nues # All rights reserved.
+# Copyright 2017-2020 Rob van Nues # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
 # permitted provided that the following conditions are met:
@@ -22,13 +22,13 @@
 #  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-PRGNAM=samtools
-VERSION=${VERSION:-1.9}
+PRGNAM=samtools			
+VERSION=${VERSION:-1.10}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
-# Some applications still rely on the legacy samtools API instead of using htslib
-# exclusively, in that case, install the headers in /usr/include/bam and the static
+# Some applications still rely on the legacy samtools API instead of using htslib 
+# exclusively, in that case, install the headers in /usr/include/bam and the static 
 # libbam library as well by declaring (uncommenting):
 #SAMLIB="yes"
 # and commenting out:
@@ -96,6 +96,17 @@ CXXFLAGS="$SLKCFLAGS" \
 make
 make install DESTDIR=$PKG
 
+mkdir -p $PKG/usr/share/$PRGNAM-$VERSION
+cp -a misc/*.lua $PKG/usr/share/$PRGNAM-$VERSION
+
+# include samtools-API if set above
+if [ "$SAMLIB" = "yes" ] ; then
+  mkdir -p $PKG/usr/include/bam
+  mkdir -p $PKG/usr/lib${LIBDIRSUFFIX}
+  install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}"
+  install -m644 *.h "$PKG/usr/include/bam"
+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
 
@@ -106,24 +117,11 @@ mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
   AUTHORS LICENSE README INSTALL NEWS examples \
   $PKG/usr/doc/$PRGNAM-$VERSION
+cp $CWD/README.references $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 
-mkdir -p $PKG/usr/share/$PRGNAM-$VERSION
-
-cp -a \
-  misc/*.lua \
-  $PKG/usr/share/$PRGNAM-$VERSION
-
 mkdir -p $PKG/install
 cat $CWD/slack-desc > $PKG/install/slack-desc
 
-# include samtools-API if set above
-if [ "$SAMLIB" = "yes" ] ; then
-  mkdir -p $PKG/usr/include/bam
-  mkdir -p $PKG/usr/lib${LIBDIRSUFFIX}
-  install -m644 libbam.a "$PKG/usr/lib${LIBDIRSUFFIX}"
-  install -m644 *.h "$PKG/usr/include/bam"
-fi
-
 cd $PKG
 /sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}