diff options
Diffstat (limited to 'academic/samtools/samtools.SlackBuild')
| -rw-r--r-- | academic/samtools/samtools.SlackBuild | 48 |
1 files changed, 27 insertions, 21 deletions
diff --git a/academic/samtools/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild index daa7e87daf..7efbaf3288 100644 --- a/academic/samtools/samtools.SlackBuild +++ b/academic/samtools/samtools.SlackBuild @@ -1,9 +1,9 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for samtools # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com -# Copyright 2017-2018 Rob van Nues # All rights reserved. +# Copyright 2017-2024 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: @@ -22,10 +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=samtools -VERSION=${VERSION:-1.9} +VERSION=${VERSION:-1.19.2} +HTSLIBV=${HTSLIBV:-1.19.1} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} # 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 @@ -47,7 +51,11 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} @@ -81,7 +89,7 @@ find -L . \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; # force linking to installed htslib -rm -r htslib-$VERSION +rm -r htslib-$HTSLIBV CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ @@ -96,6 +104,17 @@ 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 @@ -104,26 +123,13 @@ for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; r mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - AUTHORS LICENSE README INSTALL NEWS examples \ + AUTHORS LICENSE README NEWS.md examples \ $PKG/usr/doc/$PRGNAM-$VERSION +cp $CWD/README $PKG/usr/doc/$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} +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE |