From a09fca24b0b18297d95ea9cb51088c35dbaf9e28 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 13 Jan 2013 12:44:27 +0100 Subject: academic/t_coffee: Added (multiple sequence alignment program). Signed-off-by: Matteo Bernardini --- academic/t_coffee/README | 13 +++++ academic/t_coffee/References | 2 + academic/t_coffee/slack-desc | 19 +++++++ academic/t_coffee/t_coffee.SlackBuild | 100 ++++++++++++++++++++++++++++++++++ academic/t_coffee/t_coffee.info | 10 ++++ 5 files changed, 144 insertions(+) create mode 100644 academic/t_coffee/README create mode 100644 academic/t_coffee/References create mode 100644 academic/t_coffee/slack-desc create mode 100644 academic/t_coffee/t_coffee.SlackBuild create mode 100644 academic/t_coffee/t_coffee.info (limited to 'academic/t_coffee') diff --git a/academic/t_coffee/README b/academic/t_coffee/README new file mode 100644 index 0000000000..f5f6689f7d --- /dev/null +++ b/academic/t_coffee/README @@ -0,0 +1,13 @@ +T-Coffee is a multiple sequence alignment package. You can use +T-Coffee to align sequences or to combine the output of your +favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) +into one unique alignment (M-Coffee). + +T-Coffee can align Protein, DNA and RNA sequences. It is also able +to combine sequence information with protein structural information +3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA +secondary structures (R-Coffee). + +For detailed information and citation: +T-Coffee: A novel method for multiple sequence alignments. +Notredame, Higgins,Heringa,JMB,302(205-217)2000 diff --git a/academic/t_coffee/References b/academic/t_coffee/References new file mode 100644 index 0000000000..80febd6976 --- /dev/null +++ b/academic/t_coffee/References @@ -0,0 +1,2 @@ +T-Coffee: A novel method for multiple sequence alignments. +Notredame, Higgins,Heringa,JMB,302(205-217)2000 diff --git a/academic/t_coffee/slack-desc b/academic/t_coffee/slack-desc new file mode 100644 index 0000000000..6db4a674f6 --- /dev/null +++ b/academic/t_coffee/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 ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +t_coffee: t_coffee (A multiple sequence alignment program) +t_coffee: +t_coffee: T-Coffee is a multiple sequence alignment package. You can use +t_coffee: T-Coffee to align sequences or to combine the output of your +t_coffee: favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) +t_coffee: into one unique alignment (M-Coffee). +t_coffee: +t_coffee: Home: http://www.tcoffee.org/ +t_coffee: References: /usr/doc/t_coffee-$VERSION/References +t_coffee: +t_coffee: diff --git a/academic/t_coffee/t_coffee.SlackBuild b/academic/t_coffee/t_coffee.SlackBuild new file mode 100644 index 0000000000..fc66530a24 --- /dev/null +++ b/academic/t_coffee/t_coffee.SlackBuild @@ -0,0 +1,100 @@ +#!/bin/sh + +# Slackware build script for t_coffee + +# Copyright 2013 Petar Petrov, ppetrov@paju.oulu.fi +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +PRGNAM=t_coffee +VERSION=${VERSION:-9.03.r1318} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=T-COFFEE_distribution_Version + +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 {} \; + +cd t_coffee_source + +CFLAGS="$SLKCFLAGS" \ +CC="gcc" \ +FCC="gfortran" \ +make -i all + +install -D -m755 $PRGNAM $PKG/usr/bin/$PRGNAM +install -D -m755 TMalign $PKG/usr/bin/TMalign + +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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + install license.txt \ + $PKG/usr/doc/$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/t_coffee/t_coffee.info b/academic/t_coffee/t_coffee.info new file mode 100644 index 0000000000..6f358323cb --- /dev/null +++ b/academic/t_coffee/t_coffee.info @@ -0,0 +1,10 @@ +PRGNAM="t_coffee" +VERSION="9.03.r1318" +HOMEPAGE="http://www.tcoffee.org/" +DOWNLOAD="http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_9.03.r1318.tar.gz" +MD5SUM="933829c93ec8a2cb30a4e486e9252d88" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" -- cgit v1.2.3