diff options
Diffstat (limited to 'academic/bowtie2/bowtie2.SlackBuild')
| -rw-r--r-- | academic/bowtie2/bowtie2.SlackBuild | 29 |
1 files changed, 17 insertions, 12 deletions
diff --git a/academic/bowtie2/bowtie2.SlackBuild b/academic/bowtie2/bowtie2.SlackBuild index 43c3392d901f5..f113b58359cdc 100644 --- a/academic/bowtie2/bowtie2.SlackBuild +++ b/academic/bowtie2/bowtie2.SlackBuild @@ -3,6 +3,8 @@ # Slackware build script for bowtie2 # Copyright 2013-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2018 Rob van Nues sborg63@disroot.org +# # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,14 +24,14 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -PRGNAM=bowtie2 -VERSION=${VERSION:-2.1.0} +PRGNAM=bowtie2 +VERSION=${VERSION:-2.3.4.3} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -40,8 +42,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -60,7 +62,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM-$VERSION -unzip $CWD/$PRGNAM-$VERSION-source.zip +tar -xvzf $CWD/$PRGNAM-$VERSION.tar.gz cd $PRGNAM-$VERSION chown -R root:root . find -L . \ @@ -69,16 +71,20 @@ 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 {} \; - #Use our FLAGS -sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile +#sed -i "/RELEASE_FLAGS/s/=/+=/" Makefile -RELEASE_FLAGS="$SLKCFLAGS" \ +RELEASE_FLAGS+="$SLKCFLAGS" \ make install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM -install -D -m755 $PRGNAM-align $PKG/usr/bin/$PRGNAM-align +install -D -m755 $PRGNAM-align-l $PKG/usr/bin/$PRGNAM-align-l +install -D -m755 $PRGNAM-build-l $PKG/usr/bin/$PRGNAM-build-l +install -D -m755 $PRGNAM-align-s $PKG/usr/bin/$PRGNAM-align-s +install -D -m755 $PRGNAM-build-s $PKG/usr/bin/$PRGNAM-build-s install -D -m755 $PRGNAM-build $PKG/usr/bin/$PRGNAM-build +install -D -m755 $PRGNAM-inspect-l $PKG/usr/bin/$PRGNAM-inspect-l +install -D -m755 $PRGNAM-inspect-s $PKG/usr/bin/$PRGNAM-inspect-s install -D -m755 $PRGNAM-inspect $PKG/usr/bin/$PRGNAM-inspect # Copy examples and scripts @@ -86,7 +92,7 @@ mkdir -p $PKG/usr/share/$PRGNAM cp -a \ example scripts \ $PKG/usr/share/$PRGNAM - + # Let's compress the reads and indexes gzip $PKG/usr/share/$PRGNAM/example/reads/*.fq gzip $PKG/usr/share/$PRGNAM/example/index/*.bt2 @@ -99,7 +105,6 @@ cp -a \ AUTHORS LICENSE MANUAL NEWS TUTORIAL VERSION doc \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild -cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc |