From f3528ad44c025dca731e12ae3cb13875a28da5a1 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Thu, 8 Sep 2022 22:18:25 +0100 Subject: academic/prank-msa: Added (probabilistic multiple alignment program) Signed-off-by: Dave Woodfall --- academic/prank-msa/README | 32 ++++++++++ academic/prank-msa/prank-msa.SlackBuild | 110 ++++++++++++++++++++++++++++++++ academic/prank-msa/prank-msa.info | 10 +++ academic/prank-msa/slack-desc | 19 ++++++ 4 files changed, 171 insertions(+) create mode 100644 academic/prank-msa/README create mode 100644 academic/prank-msa/prank-msa.SlackBuild create mode 100644 academic/prank-msa/prank-msa.info create mode 100644 academic/prank-msa/slack-desc diff --git a/academic/prank-msa/README b/academic/prank-msa/README new file mode 100644 index 0000000000..03d714280f --- /dev/null +++ b/academic/prank-msa/README @@ -0,0 +1,32 @@ +PRANK: Probabilistic Alignment Kit + +PRANK is a probabilistic multiple alignment program for DNA, codon and +amino-acid sequences. It is based on a novel algorithm that treats +insertions correctly and avoids over-estimation of the number of +deletion events. + +In addition, PRANK borrows ideas from maximum likelihood (ML) methods +used in phylogenetics and correctly takes into account the evolutionary +distances between sequences. + +Lastly, PRANK allows for defining a potential structure for sequences to +be aligned and then, simultaneously with the alignment, predicts the +locations of structural units in the sequences. + +NOTE! +The dependencies listed in the REQUIRED field are not needed for +building PRANK. They are, however, highly recommended for the complete +functionality of the program: + +1) Progressive alignment requires a guide tree. If no tree is provided, +PRANK constructs one by calling MAFFT to make a quick alignment and +infers an NJ tree from the evolutionary distances based on that. + +2) The standard PRANK algorithm is based on an exhaustive search of the +best pairwise solution. PRANK uses Exonerate to anchor the pairwise +alignments and thus speed up the process. + +3) To improve the ancestral reconstruction, PRANK uses BppAncestor from +the BppSuite. + +NOTE 2: This will not build on a 32bit system. diff --git a/academic/prank-msa/prank-msa.SlackBuild b/academic/prank-msa/prank-msa.SlackBuild new file mode 100644 index 0000000000..a3c6791cdd --- /dev/null +++ b/academic/prank-msa/prank-msa.SlackBuild @@ -0,0 +1,110 @@ +#!/bin/bash + +# Slackware build script for prank-msa + +# Copyright 2017-2022 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. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=prank-msa +SRCNAM=prank.source +VERSION=${VERSION:-170427} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$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 $PRGNAM +tar xvf $CWD/${SRCNAM}.${VERSION}.tgz +cd $PRGNAM +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 {} \; + +cd src + +# Use our FLAGS +sed -i "/^CFLAGS/s/=/+=/" Makefile +sed -i "/^CXXFLAGS/s/=/+=/" Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make + +# Install the binary +install -D -m755 prank $PKG/usr/bin/prank + +# Place the man page in its proper location +install -D -m644 prank.1 $PKG/usr/man/man1/prank.1 + +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 + +find $PKG/usr/man -type f -exec gzip -9 {} \; +for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a ../VERSION_HISTORY $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +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 diff --git a/academic/prank-msa/prank-msa.info b/academic/prank-msa/prank-msa.info new file mode 100644 index 0000000000..ab3041d52b --- /dev/null +++ b/academic/prank-msa/prank-msa.info @@ -0,0 +1,10 @@ +PRGNAM="prank-msa" +VERSION="170427" +HOMEPAGE="http://wasabiapp.org/software/prank/" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="http://wasabiapp.org/download/prank/prank.source.170427.tgz" +MD5SUM_x86_64="a5cda14dc4e5efe1f14b84eb7a7caabd" +REQUIRES="bppsuite mafft exonerate" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/prank-msa/slack-desc b/academic/prank-msa/slack-desc new file mode 100644 index 0000000000..3a6b88e42b --- /dev/null +++ b/academic/prank-msa/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------------------------------------------------------| +prank-msa: prank-msa (A probabilistic multiple alignment program) +prank-msa: +prank-msa: PRANK is a probabilistic multiple alignment program for DNA, +prank-msa: codon and amino-acid sequences. +prank-msa: +prank-msa: Home: http://wasabiapp.org/software/prank/ +prank-msa: +prank-msa: +prank-msa: +prank-msa: +prank-msa: -- cgit v1.2.3