ap/EMBOSS: Upgraded to EMBOSS-6.1.0.

slackware-14.2
Damien Goutte-Gattat 13 years ago
parent b3cdbec12e
commit 3a79cbfb8e
  1. 1
      ap/EMBOSS/EMBOSS-6.0.1.tar.gz.sha1
  2. 1
      ap/EMBOSS/EMBOSS-6.1.0.tar.gz.sha1
  3. 48
      ap/EMBOSS/EMBOSS.SlackBuild

@ -1 +0,0 @@
ea6fa6e1e4222bc57e748a4d674d72d9b03475dd EMBOSS-6.0.1.tar.gz

@ -0,0 +1 @@
2f2a48d7aa66a8852c1dd531cfe061b024521c33 EMBOSS-6.1.0.tar.gz

@ -27,21 +27,22 @@
# Source package infos
NAMESRC=${NAMESRC:-EMBOSS}
VERSION=${VERSION:-6.0.1}
VERSION=${VERSION:-6.1.0}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz}
WGET=${WGET:-ftp://emboss.open-bio.org/pub/EMBOSS/$ARCHIVE}
# Build infos
NAMETGZ=${NAMETGZ:-EMBOSS}
NAMEPKG=${NAMEPKG:-EMBOSS}
BUILD=${BUILD:-2GGD}
ARCH=${ARCH:-i486}
EXT=${EXT:-txz}
JOBS=${JOBS:-1}
JDKVERSION=${JDKVERSION:-1.6.0_16} # JDK version on Slackware-13.0
# Directories
TMP=${TMP:-/tmp}
OUT=${OUT:-$TMP/build}
PKG=${PKG:-$OUT/$NAMETGZ}
JDK=${JDK:-/usr/lib/jdk1.6.0_11} # JDK home directory on Slackware 12.2
PKG=${PKG:-$OUT/$NAMEPKG}
CWD=$(pwd)
set -e
@ -57,12 +58,14 @@ if [ ! -d $TMP ]; then
fi
# Compilation flags
LIBDIRSUFFIX=""
case "$ARCH" in
i?86)
CPUOPT="-O2 -march=$ARCH -mtune=i686"
;;
x86_64)
CPUOPT="-O2 -fPIC"
LIBDIRSUFFIX="64"
;;
*)
CPUOPT="-O2"
@ -77,6 +80,15 @@ fi
sha1sum -c $ARCHIVE.sha1
NAME=$(tar ft $ARCHIVE | head -n 1 | cut -d / -f 1)
# Get REBASE data files
if [ ! -r rebase.tar.gz ]; then
wget -O embossre.enz ftp://ftp.neb.com/pub/rebase/emboss_e.908
wget -O embossre.sup ftp://ftp.neb.com/pub/rebase/emboss_s.908
wget -O embossre.ref ftp://ftp.neb.com/pub/rebase/emboss_r.908
tar czf rebase.tar.gz embossre.{enz,sup,ref}
rm embossre.{enz,sup,ref}
fi
# Compile
cd $TMP
echo "Building $ARCHIVE..."
@ -86,33 +98,25 @@ CFLAGS=$CPUOPT \
CXXFLAGS=$CPUOPT \
./configure \
--prefix=/usr \
--libdir=/usr/lib$LIBDIRSUFFIX \
--disable-dependency-tracking \
--disable-static \
--with-java=$JDK/include \
--with-javaos=$JDK/include/linux
--with-java=/usr/lib$LIBDIRSUFFIX/jdk$JDKVERSION/include \
--with-javaos=/usr/lib$LIBDIRSUFFIX/jdk$JDKVERSION/include/linux
make -j $JOBS
make install DESTDIR=$PKG
# Tweak JEmboss launch files
RUNJEMBOSS=$PKG/usr/share/EMBOSS/jemboss/runJemboss.sh
JEMBOSSPROPS=$PKG/usr/share/EMBOSS/jemboss/resources/jemboss.properties
sed -i 's|^JEMBOSS_HOME=.|JEMBOSS_HOME=/usr/share/EMBOSS/jemboss|' $RUNJEMBOSS
sed -i 's|/packages/emboss/STABLE|/usr|' $JEMBOSSPROPS
sed -i 's|^embossPath=.*$|embossPath=/usr/bin:/bin|' $JEMBOSSPROPS
chmod 755 $RUNJEMBOSS
ln -sv /usr/share/EMBOSS/jemboss/runJemboss.sh $PKG/usr/bin/jemboss
# Strip binaries
find $PKG | xargs file | grep "ELF 32-bit LSB" | cut -d : -f 1 | \
xargs strip --strip-unneeded 2> /dev/null
make install-strip DESTDIR=$PKG
# Install the documentation
mkdir -p $PKG/usr/doc/$NAME
install -m 644 \
AUTHORS COMPAT COPYING ChangeLog FAQ KNOWN_BUGS LICENSE NEWS ONEWS \
README THANKS \
PROBLEMS README THANKS \
$PKG/usr/doc/$NAME
# Install REBASE data
tar xf $CWD/rebase.tar.gz -C $PKG/usr/share/EMBOSS/data/REBASE
rm $PKG/usr/share/EMBOSS/data/REBASE/dummyfile
# Copy slack-desc file
install -D -m 644 $CWD/slack-desc $PKG/install/slack-desc
@ -121,7 +125,7 @@ cd $PKG
mkdir -p $OUT
PACKAGING="
chown root:root . -R
/sbin/makepkg -l y -c n $OUT/$NAMETGZ-$VERSION-$ARCH-$BUILD.tgz
/sbin/makepkg -l y -c n $OUT/$NAMEPKG-$VERSION-$ARCH-$BUILD.$EXT
rm -rf $PKG
rm -rf $TMP/$NAME
"

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