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-rw-r--r--academic/bowtie/bowtie.SlackBuild32
1 files changed, 13 insertions, 19 deletions
diff --git a/academic/bowtie/bowtie.SlackBuild b/academic/bowtie/bowtie.SlackBuild
index f9ba26ee43..ad3c81770e 100644
--- a/academic/bowtie/bowtie.SlackBuild
+++ b/academic/bowtie/bowtie.SlackBuild
@@ -2,7 +2,7 @@
# Slackware build script for bowtie
-# Copyright 2013-2021 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
@@ -25,8 +25,8 @@
cd $(dirname $0) ; CWD=$(pwd)
PRGNAM=bowtie
-VERSION=${VERSION:-1.3.0}
-BUILD=${BUILD:-1}
+VERSION=${VERSION:-1.3.1}
+BUILD=${BUILD:-2}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}
@@ -50,18 +50,12 @@ TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
-if [ "$ARCH" = "i586" ]; then
- SLKCFLAGS="-O2 -march=i586 -mtune=i686"
- LIBDIRSUFFIX=""
-elif [ "$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
@@ -70,8 +64,8 @@ rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $PRGNAM-$VERSION-src
-unzip $CWD/${PRGNAM}-${VERSION}-src.zip
-cd $PRGNAM-$VERSION-src
+tar xvf $CWD/${PRGNAM}-${VERSION}.tar.gz
+cd $PRGNAM-$VERSION
chown -R root:root .
find -L . \
\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
@@ -79,14 +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 {} \;
-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-build-s $PKG/usr/bin/$PRGNAM-build-s
-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