diff options
| -rw-r--r-- | academic/Gblocks/Gblocks.SlackBuild | 90 | ||||
| -rw-r--r-- | academic/Gblocks/Gblocks.info | 10 | ||||
| -rw-r--r-- | academic/Gblocks/README | 14 | ||||
| -rw-r--r-- | academic/Gblocks/References | 7 | ||||
| -rw-r--r-- | academic/Gblocks/slack-desc | 19 |
5 files changed, 140 insertions, 0 deletions
diff --git a/academic/Gblocks/Gblocks.SlackBuild b/academic/Gblocks/Gblocks.SlackBuild new file mode 100644 index 0000000000..fcb2a6006e --- /dev/null +++ b/academic/Gblocks/Gblocks.SlackBuild @@ -0,0 +1,90 @@ +#!/bin/sh + +# Slackware build script for Gblocks + +# Copyright 2011 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=Gblocks +VERSION=${VERSION:-0.91b} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i386 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" + exit 1 +fi + +# Determine the source arch +if [ "$ARCH" = "x86_64" ]; then + SRCARCH="64" +else + SRCARCH="" +fi + +# Construct the tarball name +TARNAME=${PRGNAM}_Linux${SRCARCH}_${VERSION} + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${PRGNAM}_${VERSION} +tar xvf $CWD/$TARNAME.tar.Z +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 {} \; + +install -D -m755 Gblocks $PKG/usr/bin/$PRGNAM + +mkdir -p $PKG/usr/share/$PRGNAM +cp -a more_alignments/* $PKG/usr/share/$PRGNAM + +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 Documentation/* $PKG/usr/doc/$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/Gblocks/Gblocks.info b/academic/Gblocks/Gblocks.info new file mode 100644 index 0000000000..0b50f869b1 --- /dev/null +++ b/academic/Gblocks/Gblocks.info @@ -0,0 +1,10 @@ +PRGNAM="Gblocks" +VERSION="0.91b" +HOMEPAGE="http://molevol.cmima.csic.es/castresana/Gblocks.html" +DOWNLOAD="http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux_0.91b.tar.Z" +MD5SUM="8b62e8447eaea37a86c35e1bf5996580" +DOWNLOAD_x86_64="http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z" +MD5SUM_x86_64="c2c752ae4cbfda0b8bf09e6662585252" +MAINTAINER="Petar Petrov" +EMAIL="ppetrov@paju.oulu.fi" +APPROVED="rworkman" diff --git a/academic/Gblocks/README b/academic/Gblocks/README new file mode 100644 index 0000000000..af80855a88 --- /dev/null +++ b/academic/Gblocks/README @@ -0,0 +1,14 @@ +Gblocks is a program written in ANSI C language that eliminates poorly +aligned positions and divergent regions of an alignment of DNA or +protein sequences. These positions may not be homologous or may have +been saturated by multiple substitutions and it is convenient to +eliminate them prior to phylogenetic analysis. + +The use of a program such as Gblocks reduces the necessity of manually +editing multiple alignments, makes the automation of phylogenetic +analysis of large data sets feasible and, finally, facilitates the +reproduction of the alignments and subsequent phylogenetic analysis by +other researchers. Gblocks is very fast in processing alignments and +it is therefore highly suitable for large-scale phylogenetic analyses. + +This just repackages the binaries provided from upstream. diff --git a/academic/Gblocks/References b/academic/Gblocks/References new file mode 100644 index 0000000000..3c993b48d0 --- /dev/null +++ b/academic/Gblocks/References @@ -0,0 +1,7 @@ +Talavera, G., and Castresana, J. (2007). Improvement of phylogenies +after removing divergent and ambiguously aligned blocks from protein +sequence alignments. Systematic Biology 56, 564-577. + +Castresana, J. (2000). Selection of conserved blocks from multiple +alignments for their use in phylogenetic analysis. Molecular Biology +and Evolution 17, 540-552.
\ No newline at end of file diff --git a/academic/Gblocks/slack-desc b/academic/Gblocks/slack-desc new file mode 100644 index 0000000000..99fbc635e6 --- /dev/null +++ b/academic/Gblocks/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------------------------------------------------------| +Gblocks: Gblocks (Select blocks of evolutionarily conserved sites) +Gblocks: +Gblocks: Gblocks is a program that eliminates poorly aligned positions and +Gblocks: divergent regions of an alignment of DNA or protein sequences. +Gblocks: +Gblocks: References: /usr/doc/Gblocks-$VERSION/References +Gblocks: Home: http://molevol.cmima.csic.es/castresana/Gblocks.html +Gblocks: +Gblocks: +Gblocks: +Gblocks: |