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| -rw-r--r-- | academic/cistrome-MACS/README | 16 | ||||
| -rw-r--r-- | academic/cistrome-MACS/References | 2 | ||||
| -rw-r--r-- | academic/cistrome-MACS/cistrome-MACS.SlackBuild | 95 | ||||
| -rw-r--r-- | academic/cistrome-MACS/cistrome-MACS.info | 10 | ||||
| -rw-r--r-- | academic/cistrome-MACS/slack-desc | 19 |
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diff --git a/academic/cistrome-MACS/README b/academic/cistrome-MACS/README new file mode 100644 index 0000000000..d039cfacfd --- /dev/null +++ b/academic/cistrome-MACS/README @@ -0,0 +1,16 @@ +MACS: Model-based Analysis of ChIP-Seq + +Next generation parallel sequencing technologies made chromatin +immunoprecipitation followed by sequencing (ChIP-Seq) a popular +strategy to study genome-wide protein-DNA interactions, while creating +challenges for analysis algorithms. We present Model-based Analysis of +ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer +(Illumina / Solexa). MACS empirically models the length of the +sequenced ChIP fragments, which tends to be shorter than sonication or +library construction size estimates, and uses it to improve the +spatial resolution of predicted binding sites. MACS also uses a +dynamic Poisson distribution to effectively capture local biases in +the genome sequence, allowing for more sensitive and robust +prediction. MACS compares favorably to existing ChIP-Seq peak-finding +algorithms, is publicly available open source, and can be used for +ChIP-Seq with or without control samples. diff --git a/academic/cistrome-MACS/References b/academic/cistrome-MACS/References new file mode 100644 index 0000000000..4cbc4be778 --- /dev/null +++ b/academic/cistrome-MACS/References @@ -0,0 +1,2 @@ +Zhang et al. Model-based Analysis of ChIP-Seq (MACS). +Genome Biol (2008) vol. 9 (9) pp. R137 diff --git a/academic/cistrome-MACS/cistrome-MACS.SlackBuild b/academic/cistrome-MACS/cistrome-MACS.SlackBuild new file mode 100644 index 0000000000..f22c48b227 --- /dev/null +++ b/academic/cistrome-MACS/cistrome-MACS.SlackBuild @@ -0,0 +1,95 @@ +#!/bin/sh + +# Slackware build script for cistrome-MACS + +# 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-MACS +VERSION=${VERSION:-1.4.2} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=MACS +SRCVER=1.4.2-1 + +if [ -z "$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-$SRCVER.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 \ + ChangeLog COPYING INSTALL NEW_IN_MACS14 README 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 macs14 macs14.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-MACS/cistrome-MACS.info b/academic/cistrome-MACS/cistrome-MACS.info new file mode 100644 index 0000000000..6b12d67dd3 --- /dev/null +++ b/academic/cistrome-MACS/cistrome-MACS.info @@ -0,0 +1,10 @@ +PRGNAM="cistrome-MACS" +VERSION="1.4.2" +HOMEPAGE="http://liulab.dfci.harvard.edu/MACS/" +DOWNLOAD="https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz" +MD5SUM="950dab09fe1335c8bbb34a896c21e3e2" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" diff --git a/academic/cistrome-MACS/slack-desc b/academic/cistrome-MACS/slack-desc new file mode 100644 index 0000000000..82b067d296 --- /dev/null +++ b/academic/cistrome-MACS/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-MACS: cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq) +cistrome-MACS: +cistrome-MACS: Next generation parallel sequencing technologies made chromatin +cistrome-MACS: immunoprecipitation followed by sequencing (ChIP-Seq) a popular +cistrome-MACS: strategy to study genome-wide protein-DNA interactions, while +cistrome-MACS: creating challenges for analysis algorithms. We present Model- +cistrome-MACS: based Analysis of ChIP-Seq (MACS) on short reads sequencers such +cistrome-MACS: as Genome Analyzer (Illumina / Solexa). +cistrome-MACS: +cistrome-MACS: Home: http://liulab.dfci.harvard.edu/MACS/ +cistrome-MACS: References: /usr/doc/cistrome-MACS-1.4.2/references |