diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/seaview/README | 14 | ||||
| -rw-r--r-- | academic/seaview/seaview.SlackBuild | 43 | ||||
| -rw-r--r-- | academic/seaview/seaview.desktop | 4 | ||||
| -rw-r--r-- | academic/seaview/seaview.info | 6 | ||||
| -rw-r--r-- | academic/seaview/slack-desc | 4 |
5 files changed, 47 insertions, 24 deletions
diff --git a/academic/seaview/README b/academic/seaview/README index 8e1bd893b4..21de5ab1c5 100644 --- a/academic/seaview/README +++ b/academic/seaview/README @@ -9,14 +9,17 @@ sequence alignment and molecular phylogeny. Important features are: alignment, and also allows to use any external alignment algorithm able to read and write FASTA-formatted files. -3) SeaView computes phylogenetic trees by +3) Seaview drives the Gblocks program to select blocks of + evolutionarily conserved sites. + +4) 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 +5) SeaView draws phylogenetic trees on screen, PDF or PostScript files +6) SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet. For details and citation: @@ -25,6 +28,5 @@ 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. +This requires fltk as a build dependency, but you also need clustalw, +Gblocks, PhyML, and muscle, all of which SeaView drives. diff --git a/academic/seaview/seaview.SlackBuild b/academic/seaview/seaview.SlackBuild index 6e8967e0da..238764fd43 100644 --- a/academic/seaview/seaview.SlackBuild +++ b/academic/seaview/seaview.SlackBuild @@ -1,17 +1,33 @@ #!/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. +# Copyright 2011 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. + +# Thanks to Niels Horn for correcting the CFLAGS. PRGNAM=seaview -VERSION=${VERSION:-4.3.0} +VERSION=${VERSION:-4.3.2} BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} +TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then case "$( uname -m )" in @@ -46,7 +62,7 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $PRGNAM -tar xvf $CWD/$PRGNAM.tar.gz +tar xvf $CWD/${PRGNAM}_${VERSION}.tar.gz cd $PRGNAM chown -R root:root . find . \ @@ -55,15 +71,20 @@ find . \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ -exec chmod 644 {} \; -#Use our CFLAGS +# Use our CFLAGS sed -i "/^CFLAGS/s/=/+=/" Makefile +# Point to the correct documentation path and phyml executable name +sed -i "s:#HELPFILE:HELPFILE:" Makefile +sed -i "s:/share/doc/seaview:/doc/$PRGNAM-$VERSION/:" Makefile +sed -i "s:#PHYMLNAME:PHYMLNAME:" 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 +install -D -m755 seaview $PKG/usr/bin/$PRGNAM +install -D -m644 seaview.1 $PKG/usr/man/man1/$PRGNAM.1 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/seaview/seaview.desktop b/academic/seaview/seaview.desktop index be832dc373..de14680455 100644 --- a/academic/seaview/seaview.desktop +++ b/academic/seaview/seaview.desktop @@ -1,7 +1,7 @@ [Desktop Entry] Categories=Education; Exec=seaview -Icon=seaview.xpm -Name=Seaview +Icon=seaview +Name=SeaView StartupNotify=false Type=Application diff --git a/academic/seaview/seaview.info b/academic/seaview/seaview.info index 8603a2ca39..299da38f30 100644 --- a/academic/seaview/seaview.info +++ b/academic/seaview/seaview.info @@ -1,8 +1,8 @@ PRGNAM="seaview" -VERSION="4.3.0" +VERSION="4.3.2" HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" -DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview.tar.gz" -MD5SUM="dc56d18e63c4c9110d9cf6198c86bd34" +DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview_4.3.2.tar.gz" +MD5SUM="d8b87a19d9cc4ee89478d647a6454fb2" DOWNLOAD_x86_64="" MD5SUM_x86_64="" MAINTAINER="Petar Petrov" diff --git a/academic/seaview/slack-desc b/academic/seaview/slack-desc index 901dc2c0f5..774e04f9ce 100644 --- a/academic/seaview/slack-desc +++ b/academic/seaview/slack-desc @@ -11,9 +11,9 @@ seaview: seaview: SeaView is a multiplatform, graphical user interface for multiple seaview: sequence alignment and molecular phylogeny. seaview: +seaview: References: /usr/doc/seaview-$VERSION/References +seaview: Home: http://pbil.univ-lyon1.fr/software/seaview.html seaview: seaview: seaview: seaview: -seaview: References: /usr/doc/seaview-$VERSION/References -seaview: Home: http://pbil.univ-lyon1.fr/software/seaview.html |