academic/novocraft: Added (map short reads onto reference genome).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
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Novoalign is a powerful tool designed for mapping of short reads onto a
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reference genome from Illumina, Ion Torrent, and 454 NGS platforms.
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It comes as part of a suit of programs (novocraft).
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This is a repackaging of the binaries made available by Novocraft that
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do not need a license.
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IMPORTANT
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Because of restrictions at the Novocraft website you can not download
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the package directly. You must go via the main download page.
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config() {
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NEW="$1"
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OLD="$(dirname $NEW)/$(basename $NEW .new)"
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# If there's no config file by that name, mv it over:
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if [ ! -r $OLD ]; then
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mv $NEW $OLD
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elif [ "$(cat $OLD | md5sum)" = "$(cat $NEW | md5sum)" ]; then
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# toss the redundant copy
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rm $NEW
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fi
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# Otherwise, we leave the .new copy for the admin to consider...
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}
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preserve_perms() {
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NEW="$1"
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OLD="$(dirname $NEW)/$(basename $NEW .new)"
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if [ -e $OLD ]; then
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cp -a $OLD ${NEW}.incoming
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cat $NEW > ${NEW}.incoming
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mv ${NEW}.incoming $NEW
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fi
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config $NEW
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}
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preserve_perms etc/profile.d/novocraft.sh.new
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preserve_perms etc/profile.d/novocraft.csh.new
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#!/bin/sh
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# Slackware build script for novocraft
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# Copyright 2017 Rob van Nues
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=novocraft
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VERSION=${VERSION:-3.08.00}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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EXTRAVERSION=${EXTRAVERSION:-Linux3.0.0-32}
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SRCNAM="${PRGNAM}V${VERSION}.${EXTRAVERSION}"
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" != "x86_64" ]; then
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echo "$ARCH is not supported." >&2
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exit 1
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fi
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM
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tar xvf $CWD/$SRCNAM.tar.gz
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cd $PRGNAM
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Remove parts that need a license or compiling
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rm -r *MPI* novo2maq
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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mv *.pdf *.txt $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/opt/$PRGNAM
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cp -a * $PKG/opt/$PRGNAM
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mkdir -p $PKG/etc/profile.d/
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install -D -m755 $CWD/$PRGNAM.sh.new $PKG/etc/profile.d/$PRGNAM.sh.new
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install -D -m755 $CWD/$PRGNAM.csh.new $PKG/etc/profile.d/$PRGNAM.csh.new
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cat $CWD/doinst.sh > $PKG/install/doinst.sh
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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#!/bin/csh
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setenv PATH ${PATH}:/opt/novocraft
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PRGNAM="novocraft"
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VERSION="3.08.00"
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HOMEPAGE="http://www.novocraft.com/products/novoalign/"
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DOWNLOAD="UNSUPPORTED"
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MD5SUM=""
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DOWNLOAD_x86_64="http://www.novocraft.com/support/download/download.php?filename=V3.08.00/novocraftV3.08.00.Linux3.0.0-32.tar.gz"
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MD5SUM_x86_64="6342c813732974dae1e560b99e37351d"
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REQUIRES=""
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MAINTAINER="Rob van Nues"
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EMAIL="rvnues at tesco {dot} net"
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#!/bin/sh
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export PATH="${PATH}:/opt/novocraft"
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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novocraft: novocraft (map short reads onto reference genome)
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novocraft:
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novocraft: The novocraft suit of programs contains tools like novoindex and
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novocraft: novoalign designed for mapping of short reads onto a reference
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novocraft: genome from Illumina, Ion Torrent, and 454 NGS platforms.
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novocraft:
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novocraft: This is a repackaging of the binaries made available by Novocraft
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novocraft: that do not need a license.
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novocraft:
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novocraft: http://www.novocraft.com/products/novoalign/
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novocraft:
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