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authorPetar Petrov <petar.petrov@student.oulu.fi>2014-10-01 07:50:09 +0700
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2014-10-03 10:16:51 +0700
commitfeb7ad033ae28d50901dc4e7bb81312ddfdfe887 (patch)
treef10af41b449467ca62fe30f361cfb1b91ca9357e /academic/bedtools/bedtools.SlackBuild
parentaa58ad6fb2b38abb5b0f1768bd5b9cd3bad71fb2 (diff)
downloadslackbuilds-feb7ad033ae28d50901dc4e7bb81312ddfdfe887.tar.gz
academic/bedtools: Added (genome arithmetic).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/bedtools/bedtools.SlackBuild')
-rw-r--r--academic/bedtools/bedtools.SlackBuild101
1 files changed, 101 insertions, 0 deletions
diff --git a/academic/bedtools/bedtools.SlackBuild b/academic/bedtools/bedtools.SlackBuild
new file mode 100644
index 0000000000..968e58da99
--- /dev/null
+++ b/academic/bedtools/bedtools.SlackBuild
@@ -0,0 +1,101 @@
+#!/bin/sh
+
+# Slackware build script for bedtools
+
+# Copyright 2014 Petar Petrov, petar.petrov@student.oulu.fi
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
+# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+PRGNAM=bedtools
+DIRNAM=bedtools2
+VERSION=${VERSION:-2.21.0}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+if [ -z "$ARCH" ]; then
+ case "$( uname -m )" in
+ i?86) ARCH=i486 ;;
+ arm*) ARCH=arm ;;
+ *) ARCH=$( uname -m ) ;;
+ esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i486" ]; then
+ SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+ LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+ SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+ LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+ SLKCFLAGS="-O2 -fPIC"
+ LIBDIRSUFFIX="64"
+else
+ SLKCFLAGS="-O2"
+ LIBDIRSUFFIX=""
+fi
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $DIRNAM
+tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
+cd $DIRNAM
+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 \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+# Use our CFLAGS
+sed -i "/CXXFLAGS/s/=/+=/" Makefile
+
+CXXFLAGS="$SLKCFLAGS" \
+make
+
+# Install the binary and scripts
+cd bin
+for i in * ; do
+ install -D -m755 $i $PKG/usr/bin/$i
+done
+cd ..
+
+# Copy additional data
+mkdir -p $PKG/usr/share/$PRGNAM
+cp -a data genomes scripts $PKG/usr/share/$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
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a LICENSE README.md RELEASE_HISTORY $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}