diff options
Diffstat (limited to 'academic/clustalo')
-rw-r--r-- | academic/clustalo/README | 11 | ||||
-rw-r--r-- | academic/clustalo/References | 4 | ||||
-rw-r--r-- | academic/clustalo/clustalo.SlackBuild | 88 | ||||
-rw-r--r-- | academic/clustalo/clustalo.info | 10 | ||||
-rw-r--r-- | academic/clustalo/slack-desc | 19 |
5 files changed, 132 insertions, 0 deletions
diff --git a/academic/clustalo/README b/academic/clustalo/README new file mode 100644 index 0000000000000..0c5bd4f20c662 --- /dev/null +++ b/academic/clustalo/README @@ -0,0 +1,11 @@ +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. + +This requires argtable. diff --git a/academic/clustalo/References b/academic/clustalo/References new file mode 100644 index 0000000000000..6f87dab1ea5a9 --- /dev/null +++ b/academic/clustalo/References @@ -0,0 +1,4 @@ +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 diff --git a/academic/clustalo/clustalo.SlackBuild b/academic/clustalo/clustalo.SlackBuild new file mode 100644 index 0000000000000..b515e6e446ae3 --- /dev/null +++ b/academic/clustalo/clustalo.SlackBuild @@ -0,0 +1,88 @@ +#!/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. + +PRGNAM=clustalo +VERSION=${VERSION:-1.0.3} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=clustal-omega + +if [ -z "$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 $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$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 + +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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + AUTHORS ChangeLog COPYING INSTALL 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 + +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.${PKGTYPE:-tgz} diff --git a/academic/clustalo/clustalo.info b/academic/clustalo/clustalo.info new file mode 100644 index 0000000000000..4d788f8cec151 --- /dev/null +++ b/academic/clustalo/clustalo.info @@ -0,0 +1,10 @@ +PRGNAM="clustalo" +VERSION="1.0.3" +HOMEPAGE="http://www.clustal.org/omega/" +DOWNLOAD="http://www.clustal.org/omega/clustal-omega-1.0.3.tar.gz" +MD5SUM="65587c7473db831255a4ecede9b4a747" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="Niels Horn" diff --git a/academic/clustalo/slack-desc b/academic/clustalo/slack-desc new file mode 100644 index 0000000000000..c56a756f910b5 --- /dev/null +++ b/academic/clustalo/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. Line +# up the first '|' above the ':' following the base package name, and the '|' +# on the right side marks the last column you can put a character in. You must +# make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':'. + + |-----handy-ruler------------------------------------------------------| +clustalo: clustalo (Clustal Omega) +clustalo: +clustalo: Clustal Omega allows hundreds of thousands of sequences to be +clustalo: aligned in only a few hours. +clustalo: +clustalo: +clustalo: +clustalo: +clustalo: +clustalo: References: /usr/doc/clustalo-$VERSION/References +clustalo: Home: http://www.clustal.org/omega/ |