diff options
Diffstat (limited to 'academic/samtools')
-rw-r--r-- | academic/samtools/samtools.SlackBuild | 26 | ||||
-rw-r--r-- | academic/samtools/samtools.info | 6 |
2 files changed, 20 insertions, 12 deletions
diff --git a/academic/samtools/samtools.SlackBuild b/academic/samtools/samtools.SlackBuild index da9e176475..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 2017-2020 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: @@ -22,13 +22,17 @@ # 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=${VERSION:-1.11} +VERSION=${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 +# 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: @@ -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" \ @@ -115,7 +123,7 @@ 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 @@ -124,4 +132,4 @@ mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc 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 diff --git a/academic/samtools/samtools.info b/academic/samtools/samtools.info index 2d42d9d715..eef9473b1e 100644 --- a/academic/samtools/samtools.info +++ b/academic/samtools/samtools.info @@ -1,8 +1,8 @@ PRGNAM="samtools" -VERSION="1.11" +VERSION="1.19.2" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2" -MD5SUM="9fd052652a9ceb56fc1098e63f596330" +DOWNLOAD="https://github.com/samtools/samtools/releases/download/1.19.2/samtools-1.19.2.tar.bz2" +MD5SUM="318492d95f5d8cef697442d1be996b77" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="htslib" |