From b56f1badba028b380ff81f2a6365190684af6948 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Tue, 14 Feb 2017 16:17:53 +0000 Subject: academic/CAFS_divergence: Added (functional shift clustering). Signed-off-by: David Spencer --- .../CAFS_divergence/CAFS_divergence.SlackBuild | 85 ++++++++++++++++++++++ academic/CAFS_divergence/CAFS_divergence.info | 10 +++ academic/CAFS_divergence/README | 26 +++++++ academic/CAFS_divergence/References | 4 + academic/CAFS_divergence/slack-desc | 19 +++++ 5 files changed, 144 insertions(+) create mode 100644 academic/CAFS_divergence/CAFS_divergence.SlackBuild create mode 100644 academic/CAFS_divergence/CAFS_divergence.info create mode 100644 academic/CAFS_divergence/README create mode 100644 academic/CAFS_divergence/References create mode 100644 academic/CAFS_divergence/slack-desc (limited to 'academic') diff --git a/academic/CAFS_divergence/CAFS_divergence.SlackBuild b/academic/CAFS_divergence/CAFS_divergence.SlackBuild new file mode 100644 index 0000000000..28b2385816 --- /dev/null +++ b/academic/CAFS_divergence/CAFS_divergence.SlackBuild @@ -0,0 +1,85 @@ +#!/bin/sh + +# Slackware build script for CAFS_divergence + +# Copyright 2017 Petar Petrov slackalaxy@gmail.com +# 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=CAFS_divergence +BINNAM=cafs +SYSTOS=linux +VERSION=${VERSION:-1.0} +BUILD=${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 + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf ${BINNAM}_${SYSTOS} +unzip $CWD/${BINNAM}_${SYSTOS} +cd ${BINNAM}_${SYSTOS} + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +install -D -m755 $BINNAM $PKG/usr/bin/$BINNAM + +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 $PKG/usr/share/$PRGNAM +cp -a \ + sample blosum62.tab \ + $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a ${BINNAM}_user_manual.pdf $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild +cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References + +mkdir -p $PKG/install +sed "s/@VERSION@/$VERSION/" < $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/CAFS_divergence/CAFS_divergence.info b/academic/CAFS_divergence/CAFS_divergence.info new file mode 100644 index 0000000000..b13935c2ca --- /dev/null +++ b/academic/CAFS_divergence/CAFS_divergence.info @@ -0,0 +1,10 @@ +PRGNAM="CAFS_divergence" +VERSION="1.0" +HOMEPAGE="http://bioinf.gen.tcd.ie/~faresm/software/software.html" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="http://bioinf.gen.tcd.ie/~faresm/software/files/cafs_linux.zip" +MD5SUM_x86_64="14e31a38eba7aefc054834a0c8a1ab90" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/CAFS_divergence/README b/academic/CAFS_divergence/README new file mode 100644 index 0000000000..9320c24786 --- /dev/null +++ b/academic/CAFS_divergence/README @@ -0,0 +1,26 @@ +CAFS: Clustering Analysis of Functional Shifts + +CAFS is a simple and fast method for Clustering functionally divergent (FD) +genes by Functional Category. + +The method implemented in CAFS is one of several sequence-based methods +for identifying the 'interesting' subset of substitutions that might +underpin functional divergence. These methods are based on the idea of that +functionally-important residues are highly conserved, so that evolutionary +rates tend to be low at important sites. Functional divergence can then be +identified by comparing rates (or levels of conservation) between two +clades of proteins at a homologous site. Alternatively, a significant +change in amino acid identity (such as a large, positively-charged residue +in one group of sequences versus a small, neutral residue in the other) +could indicate functional divergence even without a change in rate. + +This program analyses alignments and provides the user with the best +putative sites under functional divergence. + +NOTE: This only repackages the 64bit binary provided from upstream. A 32bit +executable is not available. + +Citing: +Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA (2011). +Proteome-wide analysis of functional divergence in bacteria: Exploring a +host of ecological adaptations. diff --git a/academic/CAFS_divergence/References b/academic/CAFS_divergence/References new file mode 100644 index 0000000000..f4291eaa33 --- /dev/null +++ b/academic/CAFS_divergence/References @@ -0,0 +1,4 @@ +Suggested citation +Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA (2011). +Proteome-wide analysis of functional divergence in bacteria: Exploring a host +of ecological adaptations. diff --git a/academic/CAFS_divergence/slack-desc b/academic/CAFS_divergence/slack-desc new file mode 100644 index 0000000000..97672b7592 --- /dev/null +++ b/academic/CAFS_divergence/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------------------------------------------------------| +CAFS_divergence: CAFS_divergence (Clustering Analysis of Functional Shifts) +CAFS_divergence: +CAFS_divergence: CAFS is a simple and fast method for Clustering functionally +CAFS_divergence: divergent (FD) genes by Functional Category. This program analyses +CAFS_divergence: alignments and provides the user with the best putative sites under +CAFS_divergence: functional divergence. +CAFS_divergence: +CAFS_divergence: Home: http://bioinf.gen.tcd.ie/~faresm/software/software.html +CAFS_divergence: References: /usr/doc/CAFS_divergence-@VERSION@/References +CAFS_divergence: +CAFS_divergence: -- cgit v1.2.3-65-gdbad