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Diffstat (limited to 'academic/clustalw')
-rw-r--r-- | academic/clustalw/README | 6 | ||||
-rw-r--r-- | academic/clustalw/References | 38 | ||||
-rw-r--r-- | academic/clustalw/clustalw.SlackBuild | 94 | ||||
-rw-r--r-- | academic/clustalw/clustalw.info | 10 | ||||
-rw-r--r-- | academic/clustalw/slack-desc | 19 |
5 files changed, 167 insertions, 0 deletions
diff --git a/academic/clustalw/README b/academic/clustalw/README new file mode 100644 index 0000000000..a65458b66d --- /dev/null +++ b/academic/clustalw/README @@ -0,0 +1,6 @@ +Clustal is a widely used, multiple sequence alignment program. This +is ClustalW, the command line tool. + +For details and citation: +Clustal W and Clustal X version 2.0, Larkin M., et al. Bioinformatics +2007 23(21):2947-2948 diff --git a/academic/clustalw/References b/academic/clustalw/References new file mode 100644 index 0000000000..657db37a3b --- /dev/null +++ b/academic/clustalw/References @@ -0,0 +1,38 @@ +References + +Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam +H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, +Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, +23, 2947-2948. + +Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson +JD. (2003). Multiple sequence alignment with the Clustal series of +programs. Nucleic Acids Res., 31, 3497-3500. + +Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. (1998). Multiple +sequence alignment with Clustal X. Trends Biochem Sci., 23, 403-405. + +Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. (1997). The +CLUSTAL_X windows interface: flexible strategies for multiple sequence +alignment aided by quality analysis tools. Nucleic Acids Res., 25, +4876-4882. + +Higgins DG, Thompson JD, Gibson TJ. (1996). Using CLUSTAL for multiple +sequence alignments. Methods Enzymol., 266, 383-402. + +Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving +the sensitivity of progressive multiple sequence alignment through +sequence weighting, position-specific gap penalties and weight matrix +choice. Nucleic Acids Res., 22, 4673-4680. + +Higgins DG. (1994). CLUSTAL V: multiple alignment of DNA and protein +sequences. Methods Mol Biol., 25, 307-318 + +Higgins DG, Bleasby AJ, Fuchs R. (1992). CLUSTAL V: improved software +for multiple sequence alignment. Comput. Appl. Biosci., 8, 189-191. + +Higgins,DG and Sharp,PM (1989). Fast and sensitive multiple sequence +alignments on a microcomputer. Comput. Appl. Biosci., 5, 151-153. + +Higgins,D.G. and Sharp,P.M. (1988). CLUSTAL: a package for performing +multiple sequence alignment on a microcomputer. Gene, 73, 237-244. diff --git a/academic/clustalw/clustalw.SlackBuild b/academic/clustalw/clustalw.SlackBuild new file mode 100644 index 0000000000..bdef830583 --- /dev/null +++ b/academic/clustalw/clustalw.SlackBuild @@ -0,0 +1,94 @@ +#!/bin/sh + +# Slackware build script for clustalw +# 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. + +PRGNAM=clustalw +VERSION=${VERSION:-2.1} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i486 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i486" ]; then + SLKCFLAGS="-O2 -march=i486 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find . \ + \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \ + -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ + -exec chmod 644 {} \; + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +make +make install DESTDIR=$PKG + +# Some programs expect the executable to be called clustalw, not clustalw2 +cd $PKG/usr/bin + ln -s clustalw2 clustalw +cd - + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +# This is empty +rm -rf $PKG/usr/share + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + COPYING COPYING.LESSER README clustalw_help \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/clustalw/clustalw.info b/academic/clustalw/clustalw.info new file mode 100644 index 0000000000..3fc948a033 --- /dev/null +++ b/academic/clustalw/clustalw.info @@ -0,0 +1,10 @@ +PRGNAM="clustalw" +VERSION="2.1" +HOMEPAGE="http://www.clustal.org/" +DOWNLOAD="http://www.clustal.org/download/current/clustalw-2.1.tar.gz" +MD5SUM="144df8440a0ae083d5167616c8ceeb41" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/clustalw/slack-desc b/academic/clustalw/slack-desc new file mode 100644 index 0000000000..3afe2bcbde --- /dev/null +++ b/academic/clustalw/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. Line +# up the first '|' above the ':' following the base package name, and the '|' +# on the right side marks the last column you can put a character in. You must +# make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':'. + + |-----handy-ruler------------------------------------------------------| +clustalw: clustalw (Multiple Sequence Alignment) +clustalw: +clustalw: CLUSTAL W: improving the sensitivity of progressive multiple sequence +clustalw: alignment through sequence weighting, position-specific gap penalties +clustalw: and weight matrix choice. +clustalw: +clustalw: +clustalw: +clustalw: +clustalw: References: /usr/doc/clustalw-$VERSION/References +clustalw: Home: http://www.clustal.org/ |