diff options
Diffstat (limited to 'academic/bcftools')
| -rw-r--r-- | academic/bcftools/bcftools.SlackBuild | 29 | ||||
| -rw-r--r-- | academic/bcftools/bcftools.info | 6 | ||||
| -rw-r--r-- | academic/bcftools/slack-desc | 4 |
3 files changed, 24 insertions, 15 deletions
diff --git a/academic/bcftools/bcftools.SlackBuild b/academic/bcftools/bcftools.SlackBuild index 7a17a33d25..b7a8433557 100644 --- a/academic/bcftools/bcftools.SlackBuild +++ b/academic/bcftools/bcftools.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash -# Slackware build script for samtools +# Slackware build script for bcftools -# Copyright 2017-2020 Rob van Nues # All rights reserved. +# Copyright 2017-2023 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: @@ -21,11 +21,14 @@ # 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=bcftools -VERSION=${VERSION:-1.11} +PRGNAM=bcftools +VERSION=${VERSION:-1.19} +HTSLIBV=${HTSLIBV:-1.19} BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -35,7 +38,13 @@ if [ -z "$ARCH" ]; then esac fi -CWD=$(pwd) +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${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} @@ -69,7 +78,7 @@ 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" \ @@ -99,7 +108,7 @@ 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 README LICENSE INSTALL NEWS \ + AUTHORS README LICENSE NEWS \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild @@ -107,4 +116,4 @@ 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/bcftools/bcftools.info b/academic/bcftools/bcftools.info index d181a29a4f..1998ed001c 100644 --- a/academic/bcftools/bcftools.info +++ b/academic/bcftools/bcftools.info @@ -1,8 +1,8 @@ PRGNAM="bcftools" -VERSION="1.11" +VERSION="1.19" HOMEPAGE="http://www.htslib.org" -DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.11/bcftools-1.11.tar.bz2" -MD5SUM="58908e9280e2a3f2c309177a43dc09af" +DOWNLOAD="https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.19.tar.bz2" +MD5SUM="9b4e8be279024d19f36bbaad1d2bdb41" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="htslib" diff --git a/academic/bcftools/slack-desc b/academic/bcftools/slack-desc index 2f85ffb7dd..f4c0b9871b 100644 --- a/academic/bcftools/slack-desc +++ b/academic/bcftools/slack-desc @@ -10,9 +10,9 @@ bcftools: bcftools (BCF calling tools) bcftools: bcftools: bcftools contains all the "vcf..." commands which previously lived in bcftools: the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and -bcftools: the samtools BCF calling from bcftools subdirectory of the previous +bcftools: the samtools BCF calling from bcftools subdirectory of the 'legacy' bcftools: samtools. BCFtools are meant as a faster replacement for most of the -bcftools: perl VCFtools commands. Bcftools comes with its own hstlib sources. +bcftools: perl VCFtools commands. bcftools: bcftools: Homepage: http://www.htslib.org bcftools: |