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academic/Gblocks: Added (Select blocks of evolutionarily conserved sites)
Signed-off-by: Robby Workman <rworkman@slackbuilds.org>
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90
academic/Gblocks/Gblocks.SlackBuild
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academic/Gblocks/Gblocks.SlackBuild
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#!/bin/sh
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# Slackware build script for Gblocks
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# Copyright 2011 Petar Petrov, ppetrov@paju.oulu.fi
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=Gblocks
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VERSION=${VERSION:-0.91b}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i386 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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set -e
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if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then
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printf "\n\n$ARCH is not supported... \n"
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exit 1
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fi
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# Determine the source arch
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if [ "$ARCH" = "x86_64" ]; then
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SRCARCH="64"
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else
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SRCARCH=""
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fi
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# Construct the tarball name
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TARNAME=${PRGNAM}_Linux${SRCARCH}_${VERSION}
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf ${PRGNAM}_${VERSION}
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tar xvf $CWD/$TARNAME.tar.Z
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cd ${PRGNAM}_${VERSION}
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chown -R root:root .
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find . \
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\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
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-exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
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-exec chmod 644 {} \;
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install -D -m755 Gblocks $PKG/usr/bin/$PRGNAM
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a more_alignments/* $PKG/usr/share/$PRGNAM
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a Documentation/* $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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10
academic/Gblocks/Gblocks.info
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academic/Gblocks/Gblocks.info
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PRGNAM="Gblocks"
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VERSION="0.91b"
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HOMEPAGE="http://molevol.cmima.csic.es/castresana/Gblocks.html"
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DOWNLOAD="http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux_0.91b.tar.Z"
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MD5SUM="8b62e8447eaea37a86c35e1bf5996580"
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DOWNLOAD_x86_64="http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z"
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MD5SUM_x86_64="c2c752ae4cbfda0b8bf09e6662585252"
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MAINTAINER="Petar Petrov"
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EMAIL="ppetrov@paju.oulu.fi"
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APPROVED="rworkman"
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14
academic/Gblocks/README
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academic/Gblocks/README
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Gblocks is a program written in ANSI C language that eliminates poorly
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aligned positions and divergent regions of an alignment of DNA or
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protein sequences. These positions may not be homologous or may have
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been saturated by multiple substitutions and it is convenient to
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eliminate them prior to phylogenetic analysis.
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The use of a program such as Gblocks reduces the necessity of manually
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editing multiple alignments, makes the automation of phylogenetic
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analysis of large data sets feasible and, finally, facilitates the
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reproduction of the alignments and subsequent phylogenetic analysis by
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other researchers. Gblocks is very fast in processing alignments and
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it is therefore highly suitable for large-scale phylogenetic analyses.
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This just repackages the binaries provided from upstream.
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7
academic/Gblocks/References
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7
academic/Gblocks/References
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Talavera, G., and Castresana, J. (2007). Improvement of phylogenies
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after removing divergent and ambiguously aligned blocks from protein
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sequence alignments. Systematic Biology 56, 564-577.
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Castresana, J. (2000). Selection of conserved blocks from multiple
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alignments for their use in phylogenetic analysis. Molecular Biology
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and Evolution 17, 540-552.
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19
academic/Gblocks/slack-desc
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19
academic/Gblocks/slack-desc
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description. Line
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# up the first '|' above the ':' following the base package name, and the '|'
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# on the right side marks the last column you can put a character in. You must
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# make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':'.
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|-----handy-ruler------------------------------------------------------|
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Gblocks: Gblocks (Select blocks of evolutionarily conserved sites)
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Gblocks:
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Gblocks: Gblocks is a program that eliminates poorly aligned positions and
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Gblocks: divergent regions of an alignment of DNA or protein sequences.
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Gblocks:
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Gblocks: References: /usr/doc/Gblocks-$VERSION/References
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Gblocks: Home: http://molevol.cmima.csic.es/castresana/Gblocks.html
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Gblocks:
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Gblocks:
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Gblocks:
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Gblocks:
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