academic/cistrome-CEAS: Added (Cis-regulatory Element Annotation).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov 2013-12-14 21:34:09 +07:00 committed by Erik Hanson
parent 94efe73619
commit c732454ecf
5 changed files with 139 additions and 0 deletions

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CEAS: Cis-regulatory Element Annotation System
This is a tool designed to characterize genome-wide protein-DNA
interaction patterns from ChIP-chip and ChIP-Seq of both sharp and
broad binding factors. As a stand-alone extension of our web
application CEAS, it provides statistics on ChIP enrichment at
important genome features such as specific chromosome, promoters, gene
bodies, or exons, and infers genes most likely to be regulated by a
binding factor. CEAS also enables biologists to visualize the average
ChIP enrichment signals over specific genomic features, allowing
continuous and broad ChIP enrichment to be perceived which might be
too subtle to detect from ChIP peaks alone.
A recommended package to install is R.

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Shin H, Liu T, Manrai AK, Liu XS. CEAS: Cis-regulatory element
annotation system. Bioinformatics 2009;25(19):2605-6.

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#!/bin/sh
# Slackware build script for cistrome-CEAS
# Copyright 2013 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=cistrome-CEAS
VERSION=${VERSION:-1.0.2}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
SRCNAM=CEAS-Package
if [ -z "$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 $SRCNAM-$VERSION
tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
cd $SRCNAM-$VERSION
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 {} \;
python setup.py install --root=$PKG
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 \
Artistic_License.pdf ChangeLog PKG-INFO\
$PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
# Ugene expects this to have the py suffix
cd $PKG/usr/bin
ln -s ceas ceas.py
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="cistrome-CEAS"
VERSION="1.0.2"
HOMEPAGE="http://liulab.dfci.harvard.edu/CEAS/"
DOWNLOAD="http://liulab.dfci.harvard.edu/CEAS/src/CEAS-Package-1.0.2.tar.gz"
MD5SUM="faf202ff613794ab9cd07f282c6e2663"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES=""
MAINTAINER="Petar Petrov"
EMAIL="petar.petrov@student.oulu.fi"

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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------------------------------------------------------|
cistrome-CEAS: cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System)
cistrome-CEAS:
cistrome-CEAS: This is a tool designed to characterize genome-wide protein-DNA
cistrome-CEAS: interaction patterns from ChIP-chip and ChIP-Seq of both sharp
cistrome-CEAS: broad binding factors.
cistrome-CEAS:
cistrome-CEAS: Home: http://liulab.dfci.harvard.edu/CEAS/
cistrome-CEAS: References: /usr/doc/cistrome-CEAS-1.0.2/References
cistrome-CEAS:
cistrome-CEAS:
cistrome-CEAS: