academic/genometools: Added (collection of bio-informatics tools).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
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282a9d6a01
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GenomeTools: efficient processing of structured genome annotations
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The GenomeTools genome analysis system is a free collection of bio-
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informatics tools (in the realm of genome informatics) for biological
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sequence analysis and presentation combined into a single binary named
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"gt". It is based on a C library named "libgenometools" which consists
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of several modules.
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GenomeTools can be used for:
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- sequence and annotation handling
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- sequence compression
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- index structure generation and access
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- annotation visualization
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- ...and much more!
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GenomeTools publication:
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G. Gremme, S. Steinbiss and S. Kurtz. GenomeTools: a comprehensive
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software library for efficient processing of structured genome
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annotations. IEEE/ACM Transactions on Computational Biology and
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Bioinformatics 2013, 10(3):645–656
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GenomeTools publication
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G. Gremme, S. Steinbiss and S. Kurtz.
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GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.
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IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013, in press.
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Published software in GenomeTools
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The GenomeTools distribution includes several published software tools:
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ltrharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons.
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D. Ellinghaus, S. Kurtz, and U. Willhoeft.
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LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons.
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BMC Bioinformatics 2008, 9:18
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tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
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S. Kurtz, A. Narechania, J.C. Stein, and D. Ware.
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A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.
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BMC Genomics 2008, 9:517
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uniquesub, a program for computing minimum unique substrings.
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S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek.
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Optimized design and assessment of whole genome tiling arrays.
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Bioinformatics 2007, 23(13):i195–i204
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AnnotationSketch, a library for drawing genome annotations.
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S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz.
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AnnotationSketch: a genome annotation drawing library.
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Bioinformatics 2009, 25(4):533–534
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ltrdigest, a software tool for automated annotation of internal features of LTR retrotransposons.
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S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz.
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Fine-grained annotation and classification of de novo predicted LTR retrotransposons.
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Nucleic Acids Research 2009, 37(21):7002–7013
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MetaGenomeThreader, a software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects.
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D.J. Schmitz-Hübsch and S. Kurtz.
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MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects.
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In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5
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GtEncseq, a compressed biosequence representation with many features.
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S. Steinbiss and S. Kurtz.
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A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences.
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IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357
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Readjoiner, a sequence assembler based on the assembly string graph framework.
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G. Gonnella and S. Kurtz.
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Readjoiner: a fast and memory efficient string graph-based sequence assembler.
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BMC Bioinformatics 2012, 13:82
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The following software tools are based on the GenomeTools library:
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FISH Oracle, a web server for visualizing cancer genomics data.
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M. Mader, R. Simon, S. Steinbiss and S. Kurtz.
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FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
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Journal of Clinical Bioinformatics 2011, 1:20
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ParsEval, a tool for comparing genome annotations.
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D.S. Standage and V.P. Brendel.
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ParsEval: parallel comparison and analysis of gene structure annotations.
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BMC Bioinformatics 2012, 13:187
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LTRsift, a graphical interface for working with LTR retrotransposon predictions.
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S. Steinbiss, S. Kastens and S. Kurtz.
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LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.
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Mobile DNA 2012, 3:18
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#!/bin/sh
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# Slackware build script for genometools
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# Copyright 2014 Petar Petrov, petar.petrov@student.oulu.fi
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=genometools
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VERSION=${VERSION:-1.5.2}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i486 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i486" ]; then
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SLKCFLAGS="-O2 -march=i486 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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set -e
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# Determine the build arch option
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if [ "$ARCH" = "x86_64" ]; then
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BUILDARCH="64bit=yes"
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else
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BUILDARCH=""
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fi
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$VERSION
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tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
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cd $PRGNAM-$VERSION
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Fix library path
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sed -i "s:lib/libgenometools:lib${LIBDIRSUFFIX}/libgenometools:g" Makefile
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sed -i "s:\$(prefix)/lib:\$(prefix)/lib${LIBDIRSUFFIX}:g" Makefile
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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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make $BUILDARCH \
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prefix=/usr
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make $BUILDARCH \
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prefix=$PKG/usr \
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install
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# Install python scripts
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cd gtpython
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python setup.py install --root=$PKG
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cd ..
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# Move this to /usr/share
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mkdir -p $PKG/usr/share/$PRGNAM
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mv $PKG/usr/bin/gtdata $PKG/usr/share/$PRGNAM
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# We don't need this
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rm -rf $PKG/usr/bin/genometools-config
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rm -rf $PKG/usr/lib${LIBDIRSUFFIX}/libgenometools.a
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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CHANGELOG CONTRIBUTORS INSTALL LICENSE README VERSION www/* \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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PRGNAM="genometools"
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VERSION="1.5.2"
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HOMEPAGE="http://genometools.org/"
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DOWNLOAD="http://genometools.org/pub/genometools-1.5.2.tar.gz"
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MD5SUM="ae9cba509a2e68b2ecbc8dcc12c2ad7b"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES=""
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MAINTAINER="Petar Petrov"
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EMAIL="petar.petrov@student.oulu.fi"
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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genometools: genometools (collection of bio-informatics tools)
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genometools:
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genometools: The GenomeTools genome analysis system is a free collection of
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genometools: bioinformatics tools (in the realm of genome informatics)
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genometools: combined into a single binary named gt. It is based on a C
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genometools: library named "libgenometools" which consists of several modules.
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genometools:
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genometools: Home: http://genometools.org/
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genometools: References: /usr/doc/genometools-1.5.2/References
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genometools:
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genometools:
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