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authorPetar Petrov <petar.petrov@student.oulu.fi>2014-03-03 01:09:31 +0700
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2014-03-03 01:22:34 +0700
commitd903bd6c78f455e0e0e14e5d97792c78c261bfb4 (patch)
tree0c340cd382d4f1318b09595809e19c9288120d48 /academic/bwa/bwa.SlackBuild
parentaf14cc8f246d85ffde76ca4f8e968f9f5a32d7bf (diff)
academic/bwa: Updated for version 0.7.7.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/bwa/bwa.SlackBuild')
-rw-r--r--academic/bwa/bwa.SlackBuild24
1 files changed, 13 insertions, 11 deletions
diff --git a/academic/bwa/bwa.SlackBuild b/academic/bwa/bwa.SlackBuild
index 6bf468ae185bd..d38dfbb9fa63f 100644
--- a/academic/bwa/bwa.SlackBuild
+++ b/academic/bwa/bwa.SlackBuild
@@ -2,7 +2,7 @@
# Slackware build script for bwa
-# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi
+# Copyright 2013-2014 Petar Petrov, petar.petrov@student.oulu.fi
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
@@ -23,7 +23,7 @@
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=bwa
-VERSION=${VERSION:-0.6.2}
+VERSION=${VERSION:-0.7.7}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
@@ -64,24 +64,26 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2
cd $PRGNAM-$VERSION
chown -R root:root .
find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
- -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
- -exec chmod 644 {} \;
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+ -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
# Use our CFLAGS/CXXFLAGS
sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile
-# This is needed for the build on 32bit system
-sed -i "s:-DHAVE_PTHREAD #-D_NO_SSE2:-DHAVE_PTHREAD -D_NO_SSE2:" Makefile
-
-CFLAGS="$SLKCFLAGS" \
+CFLAGS="$SLKCFLAGS -msse2" \
CXXFLAGS="$SLKCFLAGS" \
make
install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1
+mkdir -p $PKG/usr/share/$PRGNAM
+cp -a \
+ qualfa2fq.pl xa2multi.pl \
+ $PKG/usr/share/$PRGNAM
+
find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
@@ -90,7 +92,7 @@ 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 \
- ChangeLog COPYING README \
+ ChangeLog COPYING README.md \
$PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References