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| -rw-r--r-- | academic/cistrome-CEAS/README | 14 | ||||
| -rw-r--r-- | academic/cistrome-CEAS/References | 2 | ||||
| -rw-r--r-- | academic/cistrome-CEAS/cistrome-CEAS.SlackBuild | 94 | ||||
| -rw-r--r-- | academic/cistrome-CEAS/cistrome-CEAS.info | 10 | ||||
| -rw-r--r-- | academic/cistrome-CEAS/slack-desc | 19 |
5 files changed, 139 insertions, 0 deletions
diff --git a/academic/cistrome-CEAS/README b/academic/cistrome-CEAS/README new file mode 100644 index 0000000000..ca8504e954 --- /dev/null +++ b/academic/cistrome-CEAS/README @@ -0,0 +1,14 @@ +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. diff --git a/academic/cistrome-CEAS/References b/academic/cistrome-CEAS/References new file mode 100644 index 0000000000..993650dd13 --- /dev/null +++ b/academic/cistrome-CEAS/References @@ -0,0 +1,2 @@ +Shin H, Liu T, Manrai AK, Liu XS. CEAS: Cis-regulatory element +annotation system. Bioinformatics 2009;25(19):2605-6. diff --git a/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild b/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild new file mode 100644 index 0000000000..a06e7ed225 --- /dev/null +++ b/academic/cistrome-CEAS/cistrome-CEAS.SlackBuild @@ -0,0 +1,94 @@ +#!/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} diff --git a/academic/cistrome-CEAS/cistrome-CEAS.info b/academic/cistrome-CEAS/cistrome-CEAS.info new file mode 100644 index 0000000000..a61c58a620 --- /dev/null +++ b/academic/cistrome-CEAS/cistrome-CEAS.info @@ -0,0 +1,10 @@ +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" diff --git a/academic/cistrome-CEAS/slack-desc b/academic/cistrome-CEAS/slack-desc new file mode 100644 index 0000000000..818d214454 --- /dev/null +++ b/academic/cistrome-CEAS/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------------------------------------------------------| +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: |