From 2dc5cdbeea493aea0324266d96172aac3d8baf29 Mon Sep 17 00:00:00 2001
From: Damien Goutte-Gattat <dgouttegattat@incenp.org>
Date: Sat, 25 Dec 2010 00:00:58 +0100
Subject: [PATCH] ap/EMBOSS:  Upgraded to EMBOSS-6.3.1.

---
 ap/EMBOSS/EMBOSS-6.3.1.tar.gz.sha1 |  1 +
 ap/EMBOSS/EMBOSS.SlackBuild        | 16 +++++-----------
 2 files changed, 6 insertions(+), 11 deletions(-)
 create mode 100644 ap/EMBOSS/EMBOSS-6.3.1.tar.gz.sha1

diff --git a/ap/EMBOSS/EMBOSS-6.3.1.tar.gz.sha1 b/ap/EMBOSS/EMBOSS-6.3.1.tar.gz.sha1
new file mode 100644
index 00000000..1d885f62
--- /dev/null
+++ b/ap/EMBOSS/EMBOSS-6.3.1.tar.gz.sha1
@@ -0,0 +1 @@
+efb2e9c1c9b038432ce6bd81ee4692d5f1dc2f72  EMBOSS-6.3.1.tar.gz
diff --git a/ap/EMBOSS/EMBOSS.SlackBuild b/ap/EMBOSS/EMBOSS.SlackBuild
index 17d856a2..cd3c937e 100755
--- a/ap/EMBOSS/EMBOSS.SlackBuild
+++ b/ap/EMBOSS/EMBOSS.SlackBuild
@@ -29,13 +29,13 @@
 
 # Source package infos
 NAMESRC=${NAMESRC:-EMBOSS}
-VERSION=${VERSION:-6.2.0}
+VERSION=${VERSION:-6.3.1}
 ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz}
 WGET=${WGET:-ftp://emboss.open-bio.org/pub/EMBOSS/$ARCHIVE}
 
 # Build infos
 NAMEPKG=${NAMEPKG:-EMBOSS}
-BUILD=${BUILD:-2GGD}
+BUILD=${BUILD:-1GGD}
 ARCH=${ARCH:-$(uname -m | sed 's/^i?86$/i486/;s/^arm.*/arm/')}
 EXT=${EXT:-txz}
 JOBS=${JOBS:-1}
@@ -94,11 +94,6 @@ if [ ! -r rebase.tar.gz ]; then
 fi
 
 # Compile
-# EMBOSS insists on using its own copies of some available libraries
-# such as zlib, expat and pcre. I do not want to start patching the
-# build system heavily (as Debian or Fedora seem to do), so at least
-# I need to prevent replacing the system headers, hence the
-# --includedir=/usr/include/EMBOSS to isolate EMBOSS headers.
 cd $TMP
 echo "Building $ARCHIVE..."
 tar xf $CWD/$ARCHIVE
@@ -112,6 +107,7 @@ CXXFLAGS=$CPUOPT \
   $ENABLE64 \
   --disable-dependency-tracking \
   --disable-static \
+  --enable-systemlibs \
   --with-java=/usr/lib$LIBDIRSUFFIX/jdk$JDKVERSION/include \
   --with-javaos=/usr/lib$LIBDIRSUFFIX/jdk$JDKVERSION/include/linux
 make -j $JOBS
@@ -119,10 +115,8 @@ make install-strip DESTDIR=$PKG
 
 # Install the documentation
 mkdir -p $PKG/usr/doc/$NAME
-install -m 644 \
-  AUTHORS COMPAT COPYING ChangeLog FAQ KNOWN_BUGS LICENSE NEWS ONEWS \
-  PROBLEMS README THANKS \
-  $PKG/usr/doc/$NAME
+install -m 644 AUTHORS COMPAT COPYING ChangeLog FAQ KNOWN_BUGS LICENSE NEWS \
+  ONEWS PROBLEMS README THANKS $PKG/usr/doc/$NAME
 
 # Install REBASE data
 tar xf $CWD/rebase.tar.gz -C $PKG/usr/share/EMBOSS/data/REBASE