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academic/ugene: Added (unified bioinformatics toolkit).
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>
This commit is contained in:
Petar Petrov
dsomero
parent
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commit
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5 changed files with 172 additions and 0 deletions
40
academic/ugene/README
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40
academic/ugene/README
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Unipro UGENE is a multiplatform open-source software with the main
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goal of assisting molecular biologists without much expertise in
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bioinformatics to manage, analyze and visualize their data.
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UGENE integrates widely used bioinformatics tools within a common user
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interface. The toolkit supports multiple biological data formats and
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allows the retrieval of data from remote data sources. It provides
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visualization modules for biological objects such as:
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- annotated genome sequences;
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- Next Generation Sequencing (NGS) assembly data;
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- multiple sequence alignments;
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- phylogenetic trees;
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- 3D structures.
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Most of the integrated algorithms are tuned for maximum performance by
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the usage of multithreading and special processor instructions. UGENE
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includes a visual environment for creating reusable workflows that can
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be launched on local resources or in a High Performance Computing
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(HPC) environment. UGENE is written in C++ using the Qt framework. The
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built-in plugin system and structured UGENE API make it possible to
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extend the toolkit with new functionality.
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CITING:
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If you use UGENE in your work, please quote this publication:
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Unipro UGENE: a unified bioinformatics toolkit
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Konstantin Okonechnikov, Olga Golosova, Mikhail Fursov, the UGENE team
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Bioinformatics 2012 28: 1166-1167 doi: 10.1093/bioinformatics/bts091
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NOTE!
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While not needed for building of UGENE, the dependencies listed as
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"REQUIRED" are highly recommended for the complete functionality of
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the program. UGENE will also drive spidey if you have it installed,
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but keep in mind that it is available only as a 32-bit binary.
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NOTE ABOUT CUDA:
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UGENE is built without CUDA support and CUDA-BLAST is not included
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among the "REQUIRED", either. Simply, I do not have the hardware. If
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someone is interested in such functionality and can offer help with
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the script, please contact me.
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3
academic/ugene/doinst.sh
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academic/ugene/doinst.sh
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if [ -x /usr/bin/update-desktop-database ]; then
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/usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
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fi
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19
academic/ugene/slack-desc
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academic/ugene/slack-desc
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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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ugene: ugene (A unified bioinformatics toolkit)
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ugene:
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ugene: Unipro UGENE is a multiplatform open-source software with the main
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ugene: goal of assisting molecular biologists without much expertise in
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ugene: bioinformatics to manage, analyze and visualize their data.
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ugene: UGENE integrates widely used bioinformatics tools within a common
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ugene: user nterface. The toolkit supports multiple biological data formats
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ugene: and allows the retrieval of data from remote data sources.
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ugene:
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ugene: Home: http://ugene.unipro.ru/
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ugene: References: /usr/doc/ugene-$VERSION/References
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100
academic/ugene/ugene.SlackBuild
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academic/ugene/ugene.SlackBuild
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#!/bin/sh
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# Slackware build script for ugene
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# Copyright 2013 Petar Petrov, ppetrov@paju.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=ugene
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VERSION=${VERSION:-1.11.4}
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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 [ "$ARCH" = "i486" ]; then
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SLKCFLAGS="-O2 -march=i486 -mtune=i686"
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LIBDIRSUFFIX=""
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QMAKECONFIG=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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QMAKECONFIG=""
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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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QMAKECONFIG="CONFIG+=64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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QMAKECONFIG=""
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fi
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set -e
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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 . \
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\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
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-exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
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-exec chmod 644 {} \;
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# Fix libraries and man pages paths
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sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri
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sed -i "s:/share/man:/man:g" src/ugene_globals.pri
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qmake $QMAKECONFIG -r \
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QMAKE_CFLAGS="$SLKCFLAGS" \
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QMAKE_CXXFLAGS="$SLKCFLAGS"
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make
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make install INSTALL_ROOT=$PKG
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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-$VERSION
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cp -a \
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build.txt COPYRIGHT LICENSE LICENSE.3rd_party \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cat $CWD/doinst.sh > $PKG/install/doinst.sh
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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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10
academic/ugene/ugene.info
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10
academic/ugene/ugene.info
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PRGNAM="ugene"
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VERSION="1.11.4"
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HOMEPAGE="http://ugene.unipro.ru/"
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DOWNLOAD="http://ugene.unipro.ru/downloads/ugene-1.11.4.tar.gz"
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MD5SUM="49e9faea1f73b688a40f275d382f4506"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="bowtie bwa cap3 clustalw mafft mrbayes ncbi-blast ncbi-blast-plus t_coffee"
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MAINTAINER="Petar Petrov"
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EMAIL="ppetrov@paju.oulu.fi"
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