academic/genometools: Added (collection of bio-informatics tools).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

5 files changed, 223 insertions, 0 deletions

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: