diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/seaview/README | 30 | ||||
| -rw-r--r-- | academic/seaview/References | 5 | ||||
| -rw-r--r-- | academic/seaview/doinst.sh | 3 | ||||
| -rw-r--r-- | academic/seaview/seaview.SlackBuild | 88 | ||||
| -rw-r--r-- | academic/seaview/seaview.desktop | 7 | ||||
| -rw-r--r-- | academic/seaview/seaview.info | 10 | ||||
| -rw-r--r-- | academic/seaview/slack-desc | 19 |
7 files changed, 162 insertions, 0 deletions
diff --git a/academic/seaview/README b/academic/seaview/README new file mode 100644 index 0000000000000..8e1bd893b4b5d --- /dev/null +++ b/academic/seaview/README @@ -0,0 +1,30 @@ +SeaView is a multiplatform, graphical user interface for multiple +sequence alignment and molecular phylogeny. Important features are: + +1) SeaView reads and writes various file formats (NEXUS, MSF, + CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences + and of phylogenetic trees. + +2) SeaView drives programs muscle or clustalw for multiple sequence + alignment, and also allows to use any external alignment algorithm + able to read and write FASTA-formatted files. + +3) SeaView computes phylogenetic trees by + a) parsimony, using PHYLIP's dnapars/protpars algorithm, + b) distance, with NJ or BioNJ algorithms on a variety of + evolutionary distances, + c) maximum likelihood, driving program PhyML 3.0. + +4) SeaView draws phylogenetic trees on screen, PDF or PostScript files +5) SeaView allows to download sequences from EMBL/GenBank/UniProt + using the Internet. + +For details and citation: +Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a +multiplatform graphical user interface for sequence alignment and +phylogenetic tree building. Molecular Biology and Evolution +27(2):221-224. + +Seaview requires fltk as a build depencency, but you need clustalw, +PhyML and muscle, which SeaView drives. All of these are available at +SlackBuilds.org. diff --git a/academic/seaview/References b/academic/seaview/References new file mode 100644 index 0000000000000..d65333fc462a7 --- /dev/null +++ b/academic/seaview/References @@ -0,0 +1,5 @@ +References: + +Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a +multiplatform graphical user interface for sequence alignment and +phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224. diff --git a/academic/seaview/doinst.sh b/academic/seaview/doinst.sh new file mode 100644 index 0000000000000..5fb28930db0b9 --- /dev/null +++ b/academic/seaview/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/seaview/seaview.SlackBuild b/academic/seaview/seaview.SlackBuild new file mode 100644 index 0000000000000..6e8967e0da371 --- /dev/null +++ b/academic/seaview/seaview.SlackBuild @@ -0,0 +1,88 @@ +#!/bin/sh + +# Slackware build script for seaview +# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and +# hereby submitted to the public domain + +# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING +# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ +# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT. + +PRGNAM=seaview +VERSION=${VERSION:-4.3.0} +BUILD=${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 + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM +tar xvf $CWD/$PRGNAM.tar.gz +cd $PRGNAM +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 {} \; + +#Use our CFLAGS +sed -i "/^CFLAGS/s/=/+=/" Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ + make + +install -D -m755 seaview $PKG/usr/bin/seaview +install -D -m644 seaview.1 $PKG/usr/man/man1/seaview.1 + +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 + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a seaview.html $PKG/usr/doc/$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/usr/share/{applications,pixmaps} +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications +cp seaview.xpm $PKG/usr/share/pixmaps + +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.${PKGTYPE:-tgz} diff --git a/academic/seaview/seaview.desktop b/academic/seaview/seaview.desktop new file mode 100644 index 0000000000000..be832dc373122 --- /dev/null +++ b/academic/seaview/seaview.desktop @@ -0,0 +1,7 @@ +[Desktop Entry] +Categories=Education; +Exec=seaview +Icon=seaview.xpm +Name=Seaview +StartupNotify=false +Type=Application diff --git a/academic/seaview/seaview.info b/academic/seaview/seaview.info new file mode 100644 index 0000000000000..8603a2ca3949d --- /dev/null +++ b/academic/seaview/seaview.info @@ -0,0 +1,10 @@ +PRGNAM="seaview" +VERSION="4.3.0" +HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" +DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview.tar.gz" +MD5SUM="dc56d18e63c4c9110d9cf6198c86bd34" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/seaview/slack-desc b/academic/seaview/slack-desc new file mode 100644 index 0000000000000..901dc2c0f556e --- /dev/null +++ b/academic/seaview/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. Line +# up the first '|' above the ':' following the base package name, and the '|' +# on the right side marks the last column you can put a character in. You must +# make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':'. + + |-----handy-ruler------------------------------------------------------| +seaview: seaview (Multiple sequence alignment and phylogeny GUI) +seaview: +seaview: SeaView is a multiplatform, graphical user interface for multiple +seaview: sequence alignment and molecular phylogeny. +seaview: +seaview: +seaview: +seaview: +seaview: +seaview: References: /usr/doc/seaview-$VERSION/References +seaview: Home: http://pbil.univ-lyon1.fr/software/seaview.html |