From 9f49c4a61f2f8372dc05a722498d9c27f978421d Mon Sep 17 00:00:00 2001
From: Petar Petrov
Date: Sun, 12 Jan 2020 21:47:48 +0700
Subject: academic/seaview: Updated for version 5.0.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/seaview/README             | 41 ++++++++++++++++---------------------
 academic/seaview/seaview.SlackBuild | 12 +++++------
 academic/seaview/seaview.info       |  8 ++++----
 3 files changed, 28 insertions(+), 33 deletions(-)

(limited to 'academic/seaview')

diff --git a/academic/seaview/README b/academic/seaview/README
index 70a537171c..e72249f563 100644
--- a/academic/seaview/README
+++ b/academic/seaview/README
@@ -1,28 +1,23 @@
 SeaView is a multiplatform, graphical user interface for multiple
-sequence alignment and molecular phylogeny. Important features are:
+sequence alignment and molecular phylogeny. Features:
 
-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 Clustal Omega (clustalo) for
-   multiple sequence alignment, and also allows to use any external
-   alignment algorithm able to read and write FASTA-formatted files.
-
-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
-
-5) SeaView prints and draws phylogenetic trees on screen, SVG, PDF or
-   PostScript files.
-
-6) SeaView allows to download sequences from EMBL/GenBank/UniProt
-   using the Internet.
+- Reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA,
+  PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic
+  trees.
+- Drives programs muscle or Clustal Omega for multiple sequence
+  alignment, and also allows to use any external alignment
+  algorithm able to read and write FASTA-formatted files.
+- Drives the Gblocks program to select blocks of evolutionarily
+  conserved sites.
+- Computes phylogenetic trees by parsimony, using PHYLIP's dnapars /
+  protpars algorithm, distance, with NJ or BioNJ algorithms on a variety
+  of evolutionary distances, maximum likelihood, driving program PhyML
+- Can use the Transfer Bootstrap Expectation method to compute the
+  bootstrap support of PhyML and distance trees.
+- Uses the Treerecs method to reconcile gene and species trees.
+- Prints and draws phylogenetic trees on screen, SVG, PDF or PostScript
+  files.
+- Allows to download sequences from EMBL / GenBank / UniProt.
 
 For details and citation:
 Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a
diff --git a/academic/seaview/seaview.SlackBuild b/academic/seaview/seaview.SlackBuild
index 2def34de14..522170872c 100644
--- a/academic/seaview/seaview.SlackBuild
+++ b/academic/seaview/seaview.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for seaview
 
-# Copyright 2011-2018 Petar Petrov slackalaxy@gmail.com
+# Copyright 2011-2020 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -26,7 +26,7 @@
 # Thanks to developer Dr. Manolo Gouy for all his help.
 
 PRGNAM=seaview
-VERSION=${VERSION:-4.7}
+VERSION=${VERSION:-5.0}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -67,10 +67,10 @@ tar xvf $CWD/${PRGNAM}_${VERSION}.tar.gz
 cd $PRGNAM
 chown -R root:root .
 find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
- -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
- -exec chmod 644 {} \;
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
 # Use our CFLAGS
 sed -i "/^CFLAGS/s/=/+=/" Makefile
diff --git a/academic/seaview/seaview.info b/academic/seaview/seaview.info
index 116ac4c44e..fc329f3fd3 100644
--- a/academic/seaview/seaview.info
+++ b/academic/seaview/seaview.info
@@ -1,10 +1,10 @@
 PRGNAM="seaview"
-VERSION="4.7"
+VERSION="5.0"
 HOMEPAGE="http://doua.prabi.fr/software/seaview/"
-DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.7.tar.gz"
-MD5SUM="9c1ee28e7f870b76991de17b22d7dfcb"
+DOWNLOAD="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_5.0.tar.gz"
+MD5SUM="d9f1a97672efb3fd24850cf542326915"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
-REQUIRES="fltk PDFlib-Lite Gblocks PhyML clustalo muscle"
+REQUIRES="fltk PDFlib-Lite Gblocks PhyML clustalo muscle treerecs"
 MAINTAINER="Petar Petrov"
 EMAIL="slackalaxy@gmail.com"
-- 
cgit v1.2.3