academic/clustalo: Updated for version 1.1.0.

Signed-off-by: dsomero <xgizzmo@slackbuilds.org>

5 files changed, 52 insertions, 29 deletions

diff --git a/academic/clustalo/README b/academic/clustalo/README
index 0c5bd4f20c662..c597a50d73d9a 100644
--- a/academic/clustalo/README
+++ b/academic/clustalo/README
@@ -1,11 +1,19 @@
-Clustal is a widely used, multiple sequence alignment program. This 
-is Clustal Omega, the latest addition to the Clustal family. It 
-offers a significant increase in scalability over previous versions, 
-allowing hundreds of thousands of sequences to be aligned in only a 
-few hours. In addition, the quality of alignments is superior to 
+Clustal is a widely used, multiple sequence alignment program. This
+is Clustal Omega, the latest addition to the Clustal family. It
+offers a significant increase in scalability over previous versions,
+allowing hundreds of thousands of sequences to be aligned in only a
+few hours. In addition, the quality of alignments is superior to
 previous versions, as measured by a range of popular benchmarks.
 
-Clustal Omega is currently a command line-only tool, and is only 
-suitable for aligning protein sequences, not DNA or RNA. 
+Clustal Omega is currently a command line-only tool, and is only
+suitable for aligning protein sequences, not DNA or RNA.
+
+If you like Clustal-Omega please cite:
+
+Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R,
+McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.
+Fast, scalable generation of high-quality protein multiple sequence
+alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11;7:539. doi:
+10.1038/msb.2011.75. PMID: 21988835.
 
 This requires argtable.
diff --git a/academic/clustalo/References b/academic/clustalo/References
index 6f87dab1ea5a9..5550bc65a1d93 100644
--- a/academic/clustalo/References
+++ b/academic/clustalo/References
@@ -1,4 +1,5 @@
-Clustal Omega is currently under peer review. Please contact the developers/authors before citing Clustal Omega:
-
-Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega
-Fabian Sievers, Andreas Wilm, David Dineen, Toby J. Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D. Thompson, Desmond G. Higgins
\ No newline at end of file
+Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R,
+McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.
+Fast, scalable generation of high-quality protein multiple sequence
+alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11;7:539. doi:
+10.1038/msb.2011.75. PMID: 21988835.
diff --git a/academic/clustalo/clustalo.SlackBuild b/academic/clustalo/clustalo.SlackBuild
index b515e6e446ae3..7b7bf09619765 100644
--- a/academic/clustalo/clustalo.SlackBuild
+++ b/academic/clustalo/clustalo.SlackBuild
@@ -1,17 +1,31 @@
 #!/bin/sh
 
 # Slackware build script for clustalo
-# 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 2011-2012  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.
 
-PRGNAM=clustalo	
-VERSION=${VERSION:-1.0.3}	
+PRGNAM=clustalo
+VERSION=${VERSION:-1.1.0}
 BUILD=${BUILD:-1}
-TAG=${TAG:-_SBo}	
+TAG=${TAG:-_SBo}
 
 SRCNAM=clustal-omega
 
@@ -76,7 +90,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  AUTHORS ChangeLog COPYING INSTALL TODO \
+  AUTHORS ChangeLog COPYING INSTALL README TODO \
   $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
diff --git a/academic/clustalo/clustalo.info b/academic/clustalo/clustalo.info
index 4d788f8cec151..1f2d746f83bfd 100644
--- a/academic/clustalo/clustalo.info
+++ b/academic/clustalo/clustalo.info
@@ -1,10 +1,10 @@
 PRGNAM="clustalo"
-VERSION="1.0.3"
+VERSION="1.1.0"
 HOMEPAGE="http://www.clustal.org/omega/"
-DOWNLOAD="http://www.clustal.org/omega/clustal-omega-1.0.3.tar.gz"
-MD5SUM="65587c7473db831255a4ecede9b4a747"
+DOWNLOAD="http://www.clustal.org/omega/clustal-omega-1.1.0.tar.gz"
+MD5SUM="187f0204ed1aa27155e4a67cc3f48912"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 MAINTAINER="Petar Petrov"
 EMAIL="ppetrov@paju.oulu.fi"
-APPROVED="Niels Horn"
+APPROVED="dsomero"
diff --git a/academic/clustalo/slack-desc b/academic/clustalo/slack-desc
index c56a756f910b5..e27173d4d5fcf 100644
--- a/academic/clustalo/slack-desc
+++ b/academic/clustalo/slack-desc
@@ -8,12 +8,12 @@
         |-----handy-ruler------------------------------------------------------|
 clustalo: clustalo (Clustal Omega)
 clustalo:
-clustalo: Clustal Omega allows hundreds of thousands of sequences to be
+clustalo: Clustal is a widely used, multiple sequence alignment program.
+clustalo: This is Clustal Omega, the latest addition to the Clustal family.
+clustalo: It offers a significant increase in scalability over previous
+clustalo: versions, allowing hundreds of thousands of sequences to be
 clustalo: aligned in only a few hours.
 clustalo:
-clustalo:
-clustalo:
-clustalo:
-clustalo:
 clustalo: References: /usr/doc/clustalo-$VERSION/References
 clustalo: Home: http://www.clustal.org/omega/
+clustalo: