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academic/seaview: Updated for version 4.3.2. 

Signed-off-by: Robby Workman <rworkman@slackbuilds.org>
This commit is contained in:
Petar Petrov 2011-12-21 23:48:59 -06:00 committed by Robby Workman
parent 27e77182ff
commit d74ce3a23f
5 changed files with 49 additions and 26 deletions
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14
academic/seaview/README
View File

@ -9,14 +9,17 @@ sequence alignment and molecular phylogeny. Important features are:
alignment, and also allows to use any external alignment algorithm alignment, and also allows to use any external alignment algorithm
able to read and write FASTA-formatted files. 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, a) parsimony, using PHYLIP's dnapars/protpars algorithm,
b) distance, with NJ or BioNJ algorithms on a variety of b) distance, with NJ or BioNJ algorithms on a variety of
evolutionary distances, evolutionary distances,
c) maximum likelihood, driving program PhyML 3.0. c) maximum likelihood, driving program PhyML 3.0.
4) SeaView draws phylogenetic trees on screen, PDF or PostScript files 5) SeaView draws phylogenetic trees on screen, PDF or PostScript files
5) SeaView allows to download sequences from EMBL/GenBank/UniProt 6) SeaView allows to download sequences from EMBL/GenBank/UniProt
using the Internet. using the Internet.
For details and citation: For details and citation:
@ -25,6 +28,5 @@ multiplatform graphical user interface for sequence alignment and
phylogenetic tree building. Molecular Biology and Evolution phylogenetic tree building. Molecular Biology and Evolution
27(2):221-224. 27(2):221-224.
Seaview requires fltk as a build depencency, but you need clustalw, This requires fltk as a build dependency, but you also need clustalw,
PhyML and muscle, which SeaView drives. All of these are available at Gblocks, PhyML, and muscle, all of which SeaView drives.
SlackBuilds.org.

43
academic/seaview/seaview.SlackBuild
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@ -1,17 +1,33 @@
#!/bin/sh #!/bin/sh
# Slackware build script for seaview # 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 # Copyright 2011 Petar Petrov, ppetrov@paju.oulu.fi
# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ # All rights reserved.
# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT. #
# 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 PRGNAM=seaview
VERSION=${VERSION:-4.3.0} VERSION=${VERSION:-4.3.2}
BUILD=${BUILD:-1} BUILD=${BUILD:-1}
TAG=${TAG:-_SBo} TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then if [ -z "$ARCH" ]; then
case "$( uname -m )" in case "$( uname -m )" in
@ -46,7 +62,7 @@ rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT mkdir -p $TMP $PKG $OUTPUT
cd $TMP cd $TMP
rm -rf $PRGNAM rm -rf $PRGNAM
tar xvf $CWD/$PRGNAM.tar.gz tar xvf $CWD/${PRGNAM}_${VERSION}.tar.gz
cd $PRGNAM cd $PRGNAM
chown -R root:root . chown -R root:root .
find . \ find . \
@ -55,15 +71,20 @@ find . \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \; -exec chmod 644 {} \;
#Use our CFLAGS # Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" Makefile 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="$SLKCFLAGS" \ CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \
make make
install -D -m755 seaview $PKG/usr/bin/seaview install -D -m755 seaview $PKG/usr/bin/$PRGNAM
install -D -m644 seaview.1 $PKG/usr/man/man1/seaview.1 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 \ 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 | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true

4
academic/seaview/seaview.desktop
View File

@ -1,7 +1,7 @@
[Desktop Entry] [Desktop Entry]
Categories=Education; Categories=Education;
Exec=seaview Exec=seaview
Icon=seaview.xpm Icon=seaview
Name=Seaview Name=SeaView
StartupNotify=false StartupNotify=false
Type=Application Type=Application

6
academic/seaview/seaview.info
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@ -1,8 +1,8 @@
PRGNAM="seaview" PRGNAM="seaview"
VERSION="4.3.0" VERSION="4.3.2"
HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html" HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview.tar.gz" DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview_4.3.2.tar.gz"
MD5SUM="dc56d18e63c4c9110d9cf6198c86bd34" MD5SUM="d8b87a19d9cc4ee89478d647a6454fb2"
DOWNLOAD_x86_64="" DOWNLOAD_x86_64=""
MD5SUM_x86_64="" MD5SUM_x86_64=""
MAINTAINER="Petar Petrov" MAINTAINER="Petar Petrov"

8
academic/seaview/slack-desc
View File

@ -11,9 +11,9 @@ seaview:
seaview: SeaView is a multiplatform, graphical user interface for multiple seaview: SeaView is a multiplatform, graphical user interface for multiple
seaview: sequence alignment and molecular phylogeny. seaview: sequence alignment and molecular phylogeny.
seaview: seaview:
seaview:
seaview:
seaview:
seaview:
seaview: References: /usr/doc/seaview-$VERSION/References seaview: References: /usr/doc/seaview-$VERSION/References
seaview: Home: http://pbil.univ-lyon1.fr/software/seaview.html seaview: Home: http://pbil.univ-lyon1.fr/software/seaview.html
seaview:
seaview:
seaview:
seaview: