From dfe48604d3b28270605a5d16b57c39fe266a7bc0 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Mon, 3 Mar 2014 01:44:21 +0700 Subject: academic/genometools: Added (collection of bio-informatics tools). Signed-off-by: Willy Sudiarto Raharjo --- academic/genometools/README | 20 +++++ academic/genometools/References | 55 +++++++++++++ academic/genometools/genometools.SlackBuild | 119 ++++++++++++++++++++++++++++ academic/genometools/genometools.info | 10 +++ academic/genometools/slack-desc | 19 +++++ 5 files changed, 223 insertions(+) create mode 100644 academic/genometools/README create mode 100644 academic/genometools/References create mode 100644 academic/genometools/genometools.SlackBuild create mode 100644 academic/genometools/genometools.info create mode 100644 academic/genometools/slack-desc (limited to 'academic') diff --git a/academic/genometools/README b/academic/genometools/README new file mode 100644 index 0000000000..6b89d4399f --- /dev/null +++ b/academic/genometools/README @@ -0,0 +1,20 @@ +GenomeTools: efficient processing of structured genome annotations + +The GenomeTools genome analysis system is a free collection of bio- +informatics tools (in the realm of genome informatics) for biological +sequence analysis and presentation combined into a single binary named +"gt". It is based on a C library named "libgenometools" which consists +of several modules. + +GenomeTools can be used for: +- sequence and annotation handling +- sequence compression +- index structure generation and access +- annotation visualization +- ...and much more! + +GenomeTools publication: +G. Gremme, S. Steinbiss and S. Kurtz. GenomeTools: a comprehensive +software library for efficient processing of structured genome +annotations. IEEE/ACM Transactions on Computational Biology and +Bioinformatics 2013, 10(3):645–656 diff --git a/academic/genometools/References b/academic/genometools/References new file mode 100644 index 0000000000..b091778a4b --- /dev/null +++ b/academic/genometools/References @@ -0,0 +1,55 @@ +GenomeTools publication +G. Gremme, S. Steinbiss and S. Kurtz. +GenomeTools: a comprehensive software library for efficient processing of structured genome annotations. +IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013, in press. +Published software in GenomeTools + +The GenomeTools distribution includes several published software tools: + + ltrharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons. + D. Ellinghaus, S. Kurtz, and U. Willhoeft. + LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons. + BMC Bioinformatics 2008, 9:18 + tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets. + S. Kurtz, A. Narechania, J.C. Stein, and D. Ware. + A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. + BMC Genomics 2008, 9:517 + uniquesub, a program for computing minimum unique substrings. + S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek. + Optimized design and assessment of whole genome tiling arrays. + Bioinformatics 2007, 23(13):i195–i204 + AnnotationSketch, a library for drawing genome annotations. + S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz. + AnnotationSketch: a genome annotation drawing library. + Bioinformatics 2009, 25(4):533–534 + ltrdigest, a software tool for automated annotation of internal features of LTR retrotransposons. + S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz. + Fine-grained annotation and classification of de novo predicted LTR retrotransposons. + Nucleic Acids Research 2009, 37(21):7002–7013 + MetaGenomeThreader, a software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects. + D.J. Schmitz-Hübsch and S. Kurtz. + MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects. + In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5 + GtEncseq, a compressed biosequence representation with many features. + S. Steinbiss and S. Kurtz. + A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences. + IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357 + Readjoiner, a sequence assembler based on the assembly string graph framework. + G. Gonnella and S. Kurtz. + Readjoiner: a fast and memory efficient string graph-based sequence assembler. + BMC Bioinformatics 2012, 13:82 + +The following software tools are based on the GenomeTools library: + + FISH Oracle, a web server for visualizing cancer genomics data. + M. Mader, R. Simon, S. Steinbiss and S. Kurtz. + FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context. + Journal of Clinical Bioinformatics 2011, 1:20 + ParsEval, a tool for comparing genome annotations. + D.S. Standage and V.P. Brendel. + ParsEval: parallel comparison and analysis of gene structure annotations. + BMC Bioinformatics 2012, 13:187 + LTRsift, a graphical interface for working with LTR retrotransposon predictions. + S. Steinbiss, S. Kastens and S. Kurtz. + LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons. + Mobile DNA 2012, 3:18 diff --git a/academic/genometools/genometools.SlackBuild b/academic/genometools/genometools.SlackBuild new file mode 100644 index 0000000000..0674148f05 --- /dev/null +++ b/academic/genometools/genometools.SlackBuild @@ -0,0 +1,119 @@ +#!/bin/sh + +# Slackware build script for genometools + +# Copyright 2014 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=genometools +VERSION=${VERSION:-1.5.2} +BUILD=${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=${OUTPUT:-/tmp} + +if [ "$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 + +# Determine the build arch option +if [ "$ARCH" = "x86_64" ]; then + BUILDARCH="64bit=yes" +else + BUILDARCH="" +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 +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 {} \; + +# Fix library path +sed -i "s:lib/libgenometools:lib${LIBDIRSUFFIX}/libgenometools:g" Makefile +sed -i "s:\$(prefix)/lib:\$(prefix)/lib${LIBDIRSUFFIX}:g" Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make $BUILDARCH \ + prefix=/usr + +make $BUILDARCH \ + prefix=$PKG/usr \ + install + +# Install python scripts +cd gtpython +python setup.py install --root=$PKG +cd .. + +# Move this to /usr/share +mkdir -p $PKG/usr/share/$PRGNAM +mv $PKG/usr/bin/gtdata $PKG/usr/share/$PRGNAM + +# We don't need this +rm -rf $PKG/usr/bin/genometools-config +rm -rf $PKG/usr/lib${LIBDIRSUFFIX}/libgenometools.a + +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 CONTRIBUTORS INSTALL LICENSE README VERSION www/* \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +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/genometools/genometools.info b/academic/genometools/genometools.info new file mode 100644 index 0000000000..473deb75ed --- /dev/null +++ b/academic/genometools/genometools.info @@ -0,0 +1,10 @@ +PRGNAM="genometools" +VERSION="1.5.2" +HOMEPAGE="http://genometools.org/" +DOWNLOAD="http://genometools.org/pub/genometools-1.5.2.tar.gz" +MD5SUM="ae9cba509a2e68b2ecbc8dcc12c2ad7b" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" diff --git a/academic/genometools/slack-desc b/academic/genometools/slack-desc new file mode 100644 index 0000000000..a318bbaac9 --- /dev/null +++ b/academic/genometools/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------------------------------------------------------| +genometools: genometools (collection of bio-informatics tools) +genometools: +genometools: The GenomeTools genome analysis system is a free collection of +genometools: bioinformatics tools (in the realm of genome informatics) +genometools: combined into a single binary named gt. It is based on a C +genometools: library named "libgenometools" which consists of several modules. +genometools: +genometools: Home: http://genometools.org/ +genometools: References: /usr/doc/genometools-1.5.2/References +genometools: +genometools: -- cgit v1.2.3