diff options
Diffstat (limited to 'academic/bowtie')
| -rw-r--r-- | academic/bowtie/bowtie.SlackBuild | 55 | ||||
| -rw-r--r-- | academic/bowtie/bowtie.info | 12 |
2 files changed, 33 insertions, 34 deletions
diff --git a/academic/bowtie/bowtie.SlackBuild b/academic/bowtie/bowtie.SlackBuild index 0f5beae851..ad3c81770e 100644 --- a/academic/bowtie/bowtie.SlackBuild +++ b/academic/bowtie/bowtie.SlackBuild @@ -1,8 +1,8 @@ -#!/bin/sh +#!/bin/bash # Slackware build script for bowtie -# Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,36 +22,40 @@ # 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=bowtie -VERSION=${VERSION:-1.0.0} -BUILD=${BUILD:-1} +VERSION=${VERSION:-1.3.1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac fi -CWD=$(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=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then +if [ "$ARCH" = "x86_64" ]; then SLKCFLAGS="-O2 -fPIC" LIBDIRSUFFIX="64" else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" + printf "\n$ARCH is unsupported by bowtie\n" + exit 1 fi set -e @@ -59,8 +63,8 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/${PRGNAM}_${VERSION}.orig.tar.gz +rm -rf $PRGNAM-$VERSION-src +tar xvf $CWD/${PRGNAM}-${VERSION}.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -69,19 +73,14 @@ 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 {} \; -# Thanks to Debian for the set of patches! -patch -p1 -i $CWD/patches/disable_bits_flag.patch -patch -p1 -i $CWD/patches/no_hash_style_both_for_mips.patch -patch -p1 -i $CWD/patches/seqan-fix-setBegin-call.patch -patch -p1 -i $CWD/patches/use-dpkg-buildflags.patch - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ +sed -i "s|-O3|$SLKCFLAGS -O3|" Makefile make install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM -install -D -m755 $PRGNAM-build $PKG/usr/bin/$PRGNAM-build -install -D -m755 $PRGNAM-inspect $PKG/usr/bin/$PRGNAM-inspect +executables=$( ls bowtie-* ) +for b in ${executables[@]}; do + install -D -m755 $b $PKG/usr/bin/$b +done # Copy genomic data, scripts and more mkdir -p $PKG/usr/share/$PRGNAM @@ -107,4 +106,4 @@ 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/bowtie/bowtie.info b/academic/bowtie/bowtie.info index 49d8c838cb..4713d9bae4 100644 --- a/academic/bowtie/bowtie.info +++ b/academic/bowtie/bowtie.info @@ -1,10 +1,10 @@ PRGNAM="bowtie" -VERSION="1.0.0" -HOMEPAGE="http://bowtie-bio.sourceforge.net/" -DOWNLOAD="https://sourceforge.net/projects/sboppetrov/files/bowtie/bowtie_1.0.0.orig.tar.gz" -MD5SUM="75d402c856b64958ec4bc0f67d011eb9" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" +VERSION="1.3.1" +HOMEPAGE="http://bowtie-bio.sourceforge.net/index.shtml" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="https://github.com/BenLangmead/bowtie/archive/v1.3.1/bowtie-1.3.1.tar.gz" +MD5SUM_x86_64="06b0377e967501ce73bca087e6c5fcb0" REQUIRES="" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" |