diff options
| -rw-r--r-- | academic/bedGraphToBigWig/README | 7 | ||||
| -rw-r--r-- | academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild | 66 | ||||
| -rw-r--r-- | academic/bedGraphToBigWig/bedGraphToBigWig.info | 10 | ||||
| -rw-r--r-- | academic/bedGraphToBigWig/slack-desc | 19 |
4 files changed, 102 insertions, 0 deletions
diff --git a/academic/bedGraphToBigWig/README b/academic/bedGraphToBigWig/README new file mode 100644 index 0000000000..81fd8910ed --- /dev/null +++ b/academic/bedGraphToBigWig/README @@ -0,0 +1,7 @@ +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. diff --git a/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild b/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild new file mode 100644 index 0000000000..b270b511bc --- /dev/null +++ b/academic/bedGraphToBigWig/bedGraphToBigWig.SlackBuild @@ -0,0 +1,66 @@ +#!/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} diff --git a/academic/bedGraphToBigWig/bedGraphToBigWig.info b/academic/bedGraphToBigWig/bedGraphToBigWig.info new file mode 100644 index 0000000000..8d10db7752 --- /dev/null +++ b/academic/bedGraphToBigWig/bedGraphToBigWig.info @@ -0,0 +1,10 @@ +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" diff --git a/academic/bedGraphToBigWig/slack-desc b/academic/bedGraphToBigWig/slack-desc new file mode 100644 index 0000000000..eeb54bf94c --- /dev/null +++ b/academic/bedGraphToBigWig/slack-desc @@ -0,0 +1,19 @@ +# 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: |