academic/bedGraphToBigWig: Added (Convert bedGraph to bigWig file)

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Petar Petrov 2016-06-05 15:32:28 +03:00 committed by Willy Sudiarto Raharjo
parent 8e29c2c3d6
commit c600a63327
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4 changed files with 102 additions and 0 deletions

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Convert bedGraph to bigWig file. Description of Big Binary Indexed
(BBI) files and visualization of next-generation sequencing experiment
results explained by W.J. Kent, PMCID: PMC2922891
This just repackages the binary distributed by the Ugene Project, part
of their External Tools package. It is hosted on Source Forge by the
SlackBuild maintainer.

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#!/bin/sh
# Slackware build script for bedGraphToBigWig
# Copyright 2016 Petar Petrov slackalaxy@gmail.com
# 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=bedGraphToBigWig
VERSION=${VERSION:-4}
BUILD=${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=${OUTPUT:-/tmp}
set -e
if [ "$ARCH" != "x86_64" ]; then
printf "\n\n$ARCH is not supported... \n"
exit 1
fi
rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $PRGNAM-$VERSION
tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
cd $PRGNAM-$VERSION
install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM
mkdir -p $PKG/usr/doc/$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}

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PRGNAM="bedGraphToBigWig"
VERSION="4"
HOMEPAGE="https://www.encodeproject.org/software/bedgraphtobigwig/"
DOWNLOAD="UNSUPPORTED"
MD5SUM=""
DOWNLOAD_x86_64="http://sourceforge.net/projects/sboppetrov/files/bedGraphToBigWig/bedGraphToBigWig-4.tar.gz"
MD5SUM_x86_64="5b012409c804b79607b675b52369d487"
REQUIRES=""
MAINTAINER="Petar Petrov"
EMAIL="slackalaxy@gmail.com"

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# HOW TO EDIT THIS FILE:
# The "handy ruler" below makes it easier to edit a package description.
# Line up the first '|' above the ':' following the base package name, and
# the '|' on the right side marks the last column you can put a character in.
# You must make exactly 11 lines for the formatting to be correct. It's also
# customary to leave one space after the ':' except on otherwise blank lines.
|-----handy-ruler------------------------------------------------------|
bedGraphToBigWig: bedGraphToBigWig (Convert bedGraph to bigWig file)
bedGraphToBigWig:
bedGraphToBigWig: Convert bedGraph to bigWig file. For more information
bedGraphToBigWig: see the links below.
bedGraphToBigWig: https://www.encodeproject.org/software/bedgraphtobigwig/
bedGraphToBigWig: http://ugene.net/external.html
bedGraphToBigWig: http://hgdownload.cse.ucsc.edu/admin/exe/
bedGraphToBigWig:
bedGraphToBigWig:
bedGraphToBigWig:
bedGraphToBigWig: