academic/clustalo: Added (protein sequence alignment program)
Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>
This commit is contained in:
Petar Petrov
Niels Horn
parent
613fec3f78
commit
102cefc4f0
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Clustal is a widely used, multiple sequence alignment program. This
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is Clustal Omega, the latest addition to the Clustal family. It
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offers a significant increase in scalability over previous versions,
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allowing hundreds of thousands of sequences to be aligned in only a
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few hours. In addition, the quality of alignments is superior to
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previous versions, as measured by a range of popular benchmarks.
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Clustal Omega is currently a command line-only tool, and is only
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suitable for aligning protein sequences, not DNA or RNA.
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This requires argtable.
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Clustal Omega is currently under peer review. Please contact the developers/authors before citing Clustal Omega:
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Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega
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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
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#!/bin/sh
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# Slackware build script for clustalo
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# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and
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# hereby submitted to the public domain
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# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING
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# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_
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# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
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PRGNAM=clustalo
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VERSION=${VERSION:-1.0.3}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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SRCNAM=clustal-omega
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i486 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( 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=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i486" ]; then
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SLKCFLAGS="-O2 -march=i486 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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set -e
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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 $SRCNAM-$VERSION
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tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
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cd $SRCNAM-$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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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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./configure \
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--prefix=/usr \
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--libdir=/usr/lib${LIBDIRSUFFIX} \
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--sysconfdir=/etc \
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--localstatedir=/var \
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--mandir=/usr/man \
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--docdir=/usr/doc/$PRGNAM-$VERSION \
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--build=$ARCH-slackware-linux
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make
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make install DESTDIR=$PKG
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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-$VERSION
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cp -a \
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AUTHORS ChangeLog COPYING INSTALL TODO \
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$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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@ -0,0 +1,10 @@
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PRGNAM="clustalo"
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VERSION="1.0.3"
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HOMEPAGE="http://www.clustal.org/omega/"
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DOWNLOAD="http://www.clustal.org/omega/clustal-omega-1.0.3.tar.gz"
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MD5SUM="65587c7473db831255a4ecede9b4a747"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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MAINTAINER="Petar Petrov"
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EMAIL="ppetrov@paju.oulu.fi"
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APPROVED="Niels Horn"
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@ -0,0 +1,19 @@
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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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clustalo: clustalo (Clustal Omega)
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clustalo:
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clustalo: Clustal Omega allows hundreds of thousands of sequences to be
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clustalo: aligned in only a few hours.
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clustalo:
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clustalo:
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clustalo:
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clustalo:
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clustalo:
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clustalo: References: /usr/doc/clustalo-$VERSION/References
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clustalo: Home: http://www.clustal.org/omega/
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