academic/seaview: Added (sequence alignment and phylogeny GUI)
Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>
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SeaView is a multiplatform, graphical user interface for multiple
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sequence alignment and molecular phylogeny. Important features are:
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1) SeaView reads and writes various file formats (NEXUS, MSF,
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CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences
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and of phylogenetic trees.
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2) SeaView drives programs muscle or clustalw for multiple sequence
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alignment, and also allows to use any external alignment algorithm
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able to read and write FASTA-formatted files.
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3) SeaView computes phylogenetic trees by
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a) parsimony, using PHYLIP's dnapars/protpars algorithm,
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b) distance, with NJ or BioNJ algorithms on a variety of
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evolutionary distances,
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c) maximum likelihood, driving program PhyML 3.0.
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4) SeaView draws phylogenetic trees on screen, PDF or PostScript files
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5) SeaView allows to download sequences from EMBL/GenBank/UniProt
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using the Internet.
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For details and citation:
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Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a
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multiplatform graphical user interface for sequence alignment and
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phylogenetic tree building. Molecular Biology and Evolution
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27(2):221-224.
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Seaview requires fltk as a build depencency, but you need clustalw,
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PhyML and muscle, which SeaView drives. All of these are available at
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SlackBuilds.org.
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References:
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Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a
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multiplatform graphical user interface for sequence alignment and
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phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224.
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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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#!/bin/sh
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# Slackware build script for seaview
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# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and
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# hereby submitted to the public domain
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# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING
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# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_
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# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
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PRGNAM=seaview
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VERSION=${VERSION:-4.3.0}
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BUILD=${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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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
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tar xvf $CWD/$PRGNAM.tar.gz
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cd $PRGNAM
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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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#Use our CFLAGS
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sed -i "/^CFLAGS/s/=/+=/" Makefile
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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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make
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install -D -m755 seaview $PKG/usr/bin/seaview
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install -D -m644 seaview.1 $PKG/usr/man/man1/seaview.1
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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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find $PKG/usr/man -type f -exec gzip -9 {} \;
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for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a seaview.html $PKG/usr/doc/$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/usr/share/{applications,pixmaps}
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cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
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cp seaview.xpm $PKG/usr/share/pixmaps
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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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[Desktop Entry]
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Categories=Education;
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Exec=seaview
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Icon=seaview.xpm
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Name=Seaview
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StartupNotify=false
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Type=Application
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PRGNAM="seaview"
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VERSION="4.3.0"
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HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
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DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview.tar.gz"
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MD5SUM="dc56d18e63c4c9110d9cf6198c86bd34"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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MAINTAINER="Petar Petrov"
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EMAIL="ppetrov@paju.oulu.fi"
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APPROVED="Niels Horn"
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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. Line
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# up the first '|' above the ':' following the base package name, and the '|'
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# on the right side marks the last column you can put a character in. You must
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# make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':'.
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|-----handy-ruler------------------------------------------------------|
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seaview: seaview (Multiple sequence alignment and phylogeny GUI)
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seaview:
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seaview: SeaView is a multiplatform, graphical user interface for multiple
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seaview: sequence alignment and molecular phylogeny.
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seaview:
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seaview:
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seaview:
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seaview:
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seaview:
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seaview: References: /usr/doc/seaview-$VERSION/References
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seaview: Home: http://pbil.univ-lyon1.fr/software/seaview.html
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