diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/ugene/README | 40 | ||||
| -rw-r--r-- | academic/ugene/doinst.sh | 3 | ||||
| -rw-r--r-- | academic/ugene/slack-desc | 19 | ||||
| -rw-r--r-- | academic/ugene/ugene.SlackBuild | 100 | ||||
| -rw-r--r-- | academic/ugene/ugene.info | 10 |
5 files changed, 172 insertions, 0 deletions
diff --git a/academic/ugene/README b/academic/ugene/README new file mode 100644 index 0000000000..713391c36c --- /dev/null +++ b/academic/ugene/README @@ -0,0 +1,40 @@ +Unipro UGENE is a multiplatform open-source software with the main +goal of assisting molecular biologists without much expertise in +bioinformatics to manage, analyze and visualize their data. + +UGENE integrates widely used bioinformatics tools within a common user +interface. The toolkit supports multiple biological data formats and +allows the retrieval of data from remote data sources. It provides +visualization modules for biological objects such as: + +- annotated genome sequences; +- Next Generation Sequencing (NGS) assembly data; +- multiple sequence alignments; +- phylogenetic trees; +- 3D structures. + +Most of the integrated algorithms are tuned for maximum performance by +the usage of multithreading and special processor instructions. UGENE +includes a visual environment for creating reusable workflows that can +be launched on local resources or in a High Performance Computing +(HPC) environment. UGENE is written in C++ using the Qt framework. The +built-in plugin system and structured UGENE API make it possible to +extend the toolkit with new functionality. + +CITING: +If you use UGENE in your work, please quote this publication: +Unipro UGENE: a unified bioinformatics toolkit +Konstantin Okonechnikov, Olga Golosova, Mikhail Fursov, the UGENE team +Bioinformatics 2012 28: 1166-1167 doi: 10.1093/bioinformatics/bts091 + +NOTE! +While not needed for building of UGENE, the dependencies listed as +"REQUIRED" are highly recommended for the complete functionality of +the program. UGENE will also drive spidey if you have it installed, +but keep in mind that it is available only as a 32-bit binary. + +NOTE ABOUT CUDA: +UGENE is built without CUDA support and CUDA-BLAST is not included +among the "REQUIRED", either. Simply, I do not have the hardware. If +someone is interested in such functionality and can offer help with +the script, please contact me. diff --git a/academic/ugene/doinst.sh b/academic/ugene/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/ugene/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/ugene/slack-desc b/academic/ugene/slack-desc new file mode 100644 index 0000000000..212ceaea7c --- /dev/null +++ b/academic/ugene/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------------------------------------------------------| +ugene: ugene (A unified bioinformatics toolkit) +ugene: +ugene: Unipro UGENE is a multiplatform open-source software with the main +ugene: goal of assisting molecular biologists without much expertise in +ugene: bioinformatics to manage, analyze and visualize their data. +ugene: UGENE integrates widely used bioinformatics tools within a common +ugene: user nterface. The toolkit supports multiple biological data formats +ugene: and allows the retrieval of data from remote data sources. +ugene: +ugene: Home: http://ugene.unipro.ru/ +ugene: References: /usr/doc/ugene-$VERSION/References diff --git a/academic/ugene/ugene.SlackBuild b/academic/ugene/ugene.SlackBuild new file mode 100644 index 0000000000..f5737d02d6 --- /dev/null +++ b/academic/ugene/ugene.SlackBuild @@ -0,0 +1,100 @@ +#!/bin/sh + +# Slackware build script for ugene + +# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=ugene +VERSION=${VERSION:-1.11.4} +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 [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -mtune=i686" + LIBDIRSUFFIX="" + QMAKECONFIG="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" + QMAKECONFIG="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" + QMAKECONFIG="CONFIG+=64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" + QMAKECONFIG="" +fi + +set -e + +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 . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +# Fix libraries and man pages paths +sed -i "s:/lib:/lib${LIBDIRSUFFIX}:g" src/ugene_globals.pri +sed -i "s:/share/man:/man:g" src/ugene_globals.pri + +qmake $QMAKECONFIG -r \ +QMAKE_CFLAGS="$SLKCFLAGS" \ +QMAKE_CXXFLAGS="$SLKCFLAGS" +make +make install INSTALL_ROOT=$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 \ + build.txt COPYRIGHT LICENSE LICENSE.3rd_party \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/ugene/ugene.info b/academic/ugene/ugene.info new file mode 100644 index 0000000000..6bb6099760 --- /dev/null +++ b/academic/ugene/ugene.info @@ -0,0 +1,10 @@ +PRGNAM="ugene" +VERSION="1.11.4" +HOMEPAGE="http://ugene.unipro.ru/" +DOWNLOAD="http://ugene.unipro.ru/downloads/ugene-1.11.4.tar.gz" +MD5SUM="49e9faea1f73b688a40f275d382f4506" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bowtie bwa cap3 clustalw mafft mrbayes ncbi-blast ncbi-blast-plus t_coffee" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" |