From 80d665841bf9045fa91a309ba8cd6cecfc42335d Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sat, 4 Feb 2017 16:40:59 +0000 Subject: [PATCH] academic/CAPS_coevolution: Added (Coevolution Analysis). Signed-off-by: David Spencer --- .../CAPS_coevolution.SlackBuild | 101 ++++++++++++++++++ .../CAPS_coevolution/CAPS_coevolution.info | 10 ++ academic/CAPS_coevolution/README | 25 +++++ academic/CAPS_coevolution/References | 14 +++ academic/CAPS_coevolution/slack-desc | 19 ++++ 5 files changed, 169 insertions(+) create mode 100644 academic/CAPS_coevolution/CAPS_coevolution.SlackBuild create mode 100644 academic/CAPS_coevolution/CAPS_coevolution.info create mode 100644 academic/CAPS_coevolution/README create mode 100644 academic/CAPS_coevolution/References create mode 100644 academic/CAPS_coevolution/slack-desc diff --git a/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild b/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild new file mode 100644 index 0000000000..99f177b84b --- /dev/null +++ b/academic/CAPS_coevolution/CAPS_coevolution.SlackBuild @@ -0,0 +1,101 @@ +#!/bin/sh + +# Slackware build script for CAPS_coevolution + +# 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=CAPS_coevolution +VERSION=${VERSION:-2.0} +BUILD=${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 + +# The zipped names of the 32bit and 64bit versions differ too much, so +# let's set them here. +BINNAM=caps +ZIP64=caps2.0_linux_x86_64-bit +ZIP32=caps2-linux +DIR32=caps-linux + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +mkdir -p $PRGNAM-$VERSION +cd $PRGNAM-$VERSION + +if [ "$ARCH" = "x86_64" ]; then + unzip $CWD/$ZIP64.zip + cd $ZIP64 +else + unzip $CWD/$ZIP32.zip + cd $DIR32 +fi + +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 structures trees \ + $PKG/usr/share/$PRGNAM + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a ${BINNAM}_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 + +# Clean this... +rm $PKG/usr/share/$PRGNAM/structures/.DS_Store + +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/CAPS_coevolution/CAPS_coevolution.info b/academic/CAPS_coevolution/CAPS_coevolution.info new file mode 100644 index 0000000000..f51aa5d3aa --- /dev/null +++ b/academic/CAPS_coevolution/CAPS_coevolution.info @@ -0,0 +1,10 @@ +PRGNAM="CAPS_coevolution" +VERSION="2.0" +HOMEPAGE="http://bioinf.gen.tcd.ie/~faresm/software/software.html" +DOWNLOAD="http://bioinf.gen.tcd.ie/~faresm/software/files/caps2-linux.zip" +MD5SUM="72f6b7b5c0f9f441c4836b1c3a678c30" +DOWNLOAD_x86_64="http://bioinf.gen.tcd.ie/~faresm/software/files/caps2.0_linux_x86_64-bit.zip" +MD5SUM_x86_64="5fc40d2cb2e95be04bd945c155fb8ad5" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/CAPS_coevolution/README b/academic/CAPS_coevolution/README new file mode 100644 index 0000000000..b0d477c7a2 --- /dev/null +++ b/academic/CAPS_coevolution/README @@ -0,0 +1,25 @@ +CAPS: Coevolution Analysis using Protein Sequences + +CAPS is aimed at measuring the coevolution between amino acid sites +belonging to the same protein (intra-molecular coevolution) or to two +functionally or physically interacting proteins (inter-molecular +coevolution). The Software implements an improved method to detect +intra-molecular coevolution as published in Genetics (Fares and Travers, +2006) and also inter-protein coevolution analysis. The improved scoring +of amino acid sites is obtained by maximum likelihood ancestral state +reconstruction along with simulations to assess significance. + +In addition, a test which assesses whether two proteins are interacting +is implemented. + +NOTE: +The script just repackages the binaries provided from upstream. + +CITING: +CAPS: coevolution analysis using protein sequences. Fares MA, McNally D. +Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535 + +The mathematical model has been described separately: +A novel method for detecting intramolecular coevolution: adding a +further dimension to selective constraints analyses. Fares MA, Travers +SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113 diff --git a/academic/CAPS_coevolution/References b/academic/CAPS_coevolution/References new file mode 100644 index 0000000000..e8236cd282 --- /dev/null +++ b/academic/CAPS_coevolution/References @@ -0,0 +1,14 @@ +If you use CAPS in your research, please include the following citations: + +CAPS: coevolution analysis using protein sequences. +Fares MA, McNally D. +Bioinformatics. 2006 Nov 15;22(22):2821-2. +PMID: 17005535 +https://www.ncbi.nlm.nih.gov/pubmed/17005535 + +The mathematical model has been described separately: +A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. +Fares MA, Travers SA. +Genetics. 2006 May;173(1):9-23. +PMID: 16547113 +https://www.ncbi.nlm.nih.gov/pubmed/16547113 diff --git a/academic/CAPS_coevolution/slack-desc b/academic/CAPS_coevolution/slack-desc new file mode 100644 index 0000000000..10791d3547 --- /dev/null +++ b/academic/CAPS_coevolution/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------------------------------------------------------| +CAPS_coevolution: CAPS_coevolution (Coevolution Analysis using Protein Sequences) +CAPS_coevolution: +CAPS_coevolution: CAPS is aimed at measuring the coevolution between amino acid +CAPS_coevolution: sites belonging to the same protein (intra-molecular coevolution) +CAPS_coevolution: or to two functionally or physically interacting proteins (inter- +CAPS_coevolution: molecular coevolution). In addition, a test which assesses +CAPS_coevolution: whether two proteins are interacting is implemented. +CAPS_coevolution: +CAPS_coevolution: Home: http://bioinf.gen.tcd.ie/~faresm/software/software.html +CAPS_coevolution: References: /usr/doc/CAPS_coevolution-2.0/References +CAPS_coevolution: