From d903bd6c78f455e0e0e14e5d97792c78c261bfb4 Mon Sep 17 00:00:00 2001
From: Petar Petrov
Date: Mon, 3 Mar 2014 01:09:31 +0700
Subject: academic/bwa: Updated for version 0.7.7.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/bwa/bwa.SlackBuild | 24 +++++++++++++-----------
 academic/bwa/bwa.info       |  8 ++++----
 2 files changed, 17 insertions(+), 15 deletions(-)

(limited to 'academic/bwa')

diff --git a/academic/bwa/bwa.SlackBuild b/academic/bwa/bwa.SlackBuild
index 6bf468ae18..d38dfbb9fa 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 0ef3c81947..6763f3f75b 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"
-- 
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