diff options
| -rw-r--r-- | academic/bwa/bwa.SlackBuild | 24 | ||||
| -rw-r--r-- | academic/bwa/bwa.info | 8 |
2 files changed, 17 insertions, 15 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 diff --git a/academic/bwa/bwa.info b/academic/bwa/bwa.info index 0ef3c81947ca0..6763f3f75b8a7 100644 --- a/academic/bwa/bwa.info +++ b/academic/bwa/bwa.info @@ -1,10 +1,10 @@ PRGNAM="bwa" -VERSION="0.6.2" +VERSION="0.7.7" HOMEPAGE="http://bio-bwa.sourceforge.net/" -DOWNLOAD="http://downloads.sourceforge.net/bio-bwa/bwa-0.6.2.tar.bz2" -MD5SUM="5e4043769ce3436f6098ec67f6e02332" +DOWNLOAD="http://downloads.sourceforge.net/bio-bwa/bwa-0.7.7.tar.bz2" +MD5SUM="0fa74b1debe42a12c2d8443dfc64ce6c" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Petar Petrov" -EMAIL="ppetrov@paju.oulu.fi" +EMAIL="petar.petrov@student.oulu.fi" |