diff options
| -rw-r--r-- | academic/clustalo/README | 22 | ||||
| -rw-r--r-- | academic/clustalo/References | 9 | ||||
| -rw-r--r-- | academic/clustalo/clustalo.SlackBuild | 32 | ||||
| -rw-r--r-- | academic/clustalo/clustalo.info | 8 | ||||
| -rw-r--r-- | academic/clustalo/slack-desc | 10 |
5 files changed, 52 insertions, 29 deletions
diff --git a/academic/clustalo/README b/academic/clustalo/README index 0c5bd4f20c..c597a50d73 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 6f87dab1ea..5550bc65a1 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 b515e6e446..7b7bf09619 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-$VERSION/References diff --git a/academic/clustalo/clustalo.info b/academic/clustalo/clustalo.info index 4d788f8cec..1f2d746f83 100644 --- a/academic/clustalo/clustalo.info +++ b/academic/clustalo/clustalo.info @@ -1,10 +1,10 @@ PRGNAM="clustalo" -VERSION="1.0.3" +VERSION="1.1.0" HOMEPAGE="http://www.clustal.org/omega/" -DOWNLOAD="http://www.clustal.org/omega/clustal-omega-1.0.3.tar.gz" -MD5SUM="65587c7473db831255a4ecede9b4a747" +DOWNLOAD="http://www.clustal.org/omega/clustal-omega-1.1.0.tar.gz" +MD5SUM="187f0204ed1aa27155e4a67cc3f48912" DOWNLOAD_x86_64="" MD5SUM_x86_64="" MAINTAINER="Petar Petrov" EMAIL="ppetrov@paju.oulu.fi" -APPROVED="Niels Horn" +APPROVED="dsomero" diff --git a/academic/clustalo/slack-desc b/academic/clustalo/slack-desc index c56a756f91..e27173d4d5 100644 --- a/academic/clustalo/slack-desc +++ b/academic/clustalo/slack-desc @@ -8,12 +8,12 @@ |-----handy-ruler------------------------------------------------------| clustalo: clustalo (Clustal Omega) clustalo: -clustalo: Clustal Omega allows hundreds of thousands of sequences to be +clustalo: Clustal is a widely used, multiple sequence alignment program. +clustalo: This is Clustal Omega, the latest addition to the Clustal family. +clustalo: It offers a significant increase in scalability over previous +clustalo: versions, allowing hundreds of thousands of sequences to be clustalo: aligned in only a few hours. clustalo: -clustalo: -clustalo: -clustalo: -clustalo: clustalo: References: /usr/doc/clustalo-$VERSION/References clustalo: Home: http://www.clustal.org/omega/ +clustalo: |