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-rw-r--r--academic/bowtie/bowtie.SlackBuild22
1 files changed, 14 insertions, 8 deletions
diff --git a/academic/bowtie/bowtie.SlackBuild b/academic/bowtie/bowtie.SlackBuild
index a4b3ce38e6..cb9ab8a4fc 100644
--- a/academic/bowtie/bowtie.SlackBuild
+++ b/academic/bowtie/bowtie.SlackBuild
@@ -2,7 +2,7 @@
# Slackware build script for bowtie
-# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi
+# Copyright 2013 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=bowtie
-VERSION=${VERSION:-0.12.9}
+VERSION=${VERSION:-1.0.0}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
@@ -60,14 +60,20 @@ rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $PRGNAM-$VERSION
-unzip $CWD/$PRGNAM-$VERSION-src.zip
+tar xvf $CWD/${PRGNAM}_${VERSION}.orig.tar.gz
cd $PRGNAM-$VERSION
chown -R root:root .
find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
- -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 {} \;
+
+# 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" \
@@ -92,7 +98,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
- AUTHORS COPYING MANUAL NEWS TUTORIAL VERSION doc \
+ 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