diff options
author | Rob van Nues <rvnues at tesco {dot} net> | 2017-09-10 19:26:09 +0100 |
---|---|---|
committer | Willy Sudiarto Raharjo <willysr@slackbuilds.org> | 2017-09-16 07:15:01 +0700 |
commit | 14c13dd569ce25a3ae01ca4fe59f9c1cafe4c9e9 (patch) | |
tree | 645db8fa41c17debcd118170c1aee9014dfcb2ee /academic/novocraft/novocraft.SlackBuild | |
parent | 87f60da8dead64a7e438ea4e1186807adb7c7212 (diff) | |
download | slackbuilds-14c13dd569ce25a3ae01ca4fe59f9c1cafe4c9e9.tar.gz |
academic/novocraft: Added (map short reads onto reference genome).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
Diffstat (limited to 'academic/novocraft/novocraft.SlackBuild')
-rw-r--r-- | academic/novocraft/novocraft.SlackBuild | 85 |
1 files changed, 85 insertions, 0 deletions
diff --git a/academic/novocraft/novocraft.SlackBuild b/academic/novocraft/novocraft.SlackBuild new file mode 100644 index 0000000000..f42c708088 --- /dev/null +++ b/academic/novocraft/novocraft.SlackBuild @@ -0,0 +1,85 @@ +#!/bin/sh + +# Slackware build script for novocraft + +# Copyright 2017 Rob van Nues +# 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=novocraft +VERSION=${VERSION:-3.08.00} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +EXTRAVERSION=${EXTRAVERSION:-Linux3.0.0-32} +SRCNAM="${PRGNAM}V${VERSION}.${EXTRAVERSION}" + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" != "x86_64" ]; then + echo "$ARCH is not supported." >&2 + exit 1 +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM +tar xvf $CWD/$SRCNAM.tar.gz +cd $PRGNAM +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 {} \; + +# Remove parts that need a license or compiling +rm -r *MPI* novo2maq + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +mv *.pdf *.txt $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/opt/$PRGNAM +cp -a * $PKG/opt/$PRGNAM + +mkdir -p $PKG/etc/profile.d/ +install -D -m755 $CWD/$PRGNAM.sh.new $PKG/etc/profile.d/$PRGNAM.sh.new +install -D -m755 $CWD/$PRGNAM.csh.new $PKG/etc/profile.d/$PRGNAM.csh.new + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} |