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academic/CAPS_coevolution: Added (Coevolution Analysis).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
1852c5a4c1
commit
80d665841b
5 changed files with 169 additions and 0 deletions
101
academic/CAPS_coevolution/CAPS_coevolution.SlackBuild
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101
academic/CAPS_coevolution/CAPS_coevolution.SlackBuild
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#!/bin/sh
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# Slackware build script for CAPS_coevolution
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# Copyright 2017 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=CAPS_coevolution
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VERSION=${VERSION:-2.0}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i386 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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set -e
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if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then
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printf "\n\n$ARCH is not supported... \n"
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exit 1
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fi
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# The zipped names of the 32bit and 64bit versions differ too much, so
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# let's set them here.
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BINNAM=caps
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ZIP64=caps2.0_linux_x86_64-bit
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ZIP32=caps2-linux
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DIR32=caps-linux
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$VERSION
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mkdir -p $PRGNAM-$VERSION
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cd $PRGNAM-$VERSION
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if [ "$ARCH" = "x86_64" ]; then
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unzip $CWD/$ZIP64.zip
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cd $ZIP64
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else
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unzip $CWD/$ZIP32.zip
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cd $DIR32
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fi
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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install -D -m755 $BINNAM $PKG/usr/bin/$BINNAM
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a \
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sample structures trees \
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$PKG/usr/share/$PRGNAM
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a ${BINNAM}_manual.pdf $PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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# Clean this...
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rm $PKG/usr/share/$PRGNAM/structures/.DS_Store
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
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10
academic/CAPS_coevolution/CAPS_coevolution.info
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academic/CAPS_coevolution/CAPS_coevolution.info
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PRGNAM="CAPS_coevolution"
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VERSION="2.0"
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HOMEPAGE="http://bioinf.gen.tcd.ie/~faresm/software/software.html"
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DOWNLOAD="http://bioinf.gen.tcd.ie/~faresm/software/files/caps2-linux.zip"
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MD5SUM="72f6b7b5c0f9f441c4836b1c3a678c30"
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DOWNLOAD_x86_64="http://bioinf.gen.tcd.ie/~faresm/software/files/caps2.0_linux_x86_64-bit.zip"
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MD5SUM_x86_64="5fc40d2cb2e95be04bd945c155fb8ad5"
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REQUIRES=""
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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25
academic/CAPS_coevolution/README
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academic/CAPS_coevolution/README
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CAPS: Coevolution Analysis using Protein Sequences
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CAPS is aimed at measuring the coevolution between amino acid sites
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belonging to the same protein (intra-molecular coevolution) or to two
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functionally or physically interacting proteins (inter-molecular
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coevolution). The Software implements an improved method to detect
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intra-molecular coevolution as published in Genetics (Fares and Travers,
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2006) and also inter-protein coevolution analysis. The improved scoring
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of amino acid sites is obtained by maximum likelihood ancestral state
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reconstruction along with simulations to assess significance.
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In addition, a test which assesses whether two proteins are interacting
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is implemented.
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NOTE:
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The script just repackages the binaries provided from upstream.
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CITING:
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CAPS: coevolution analysis using protein sequences. Fares MA, McNally D.
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Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535
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The mathematical model has been described separately:
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A novel method for detecting intramolecular coevolution: adding a
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further dimension to selective constraints analyses. Fares MA, Travers
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SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113
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14
academic/CAPS_coevolution/References
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14
academic/CAPS_coevolution/References
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If you use CAPS in your research, please include the following citations:
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CAPS: coevolution analysis using protein sequences.
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Fares MA, McNally D.
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Bioinformatics. 2006 Nov 15;22(22):2821-2.
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PMID: 17005535
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https://www.ncbi.nlm.nih.gov/pubmed/17005535
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The mathematical model has been described separately:
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A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses.
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Fares MA, Travers SA.
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Genetics. 2006 May;173(1):9-23.
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PMID: 16547113
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https://www.ncbi.nlm.nih.gov/pubmed/16547113
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19
academic/CAPS_coevolution/slack-desc
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19
academic/CAPS_coevolution/slack-desc
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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CAPS_coevolution: CAPS_coevolution (Coevolution Analysis using Protein Sequences)
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CAPS_coevolution:
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CAPS_coevolution: CAPS is aimed at measuring the coevolution between amino acid
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CAPS_coevolution: sites belonging to the same protein (intra-molecular coevolution)
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CAPS_coevolution: or to two functionally or physically interacting proteins (inter-
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CAPS_coevolution: molecular coevolution). In addition, a test which assesses
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CAPS_coevolution: whether two proteins are interacting is implemented.
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CAPS_coevolution:
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CAPS_coevolution: Home: http://bioinf.gen.tcd.ie/~faresm/software/software.html
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CAPS_coevolution: References: /usr/doc/CAPS_coevolution-2.0/References
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CAPS_coevolution:
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