From 7a9d94eb690944a6c8dbb832744a1c85728c3986 Mon Sep 17 00:00:00 2001 From: Matteo Bernardini Date: Sun, 27 Feb 2022 09:03:09 +0100 Subject: academic/prank-msa: Removed (ftb + no active maintainer). Signed-off-by: Matteo Bernardini --- academic/prank-msa/README | 32 --------- academic/prank-msa/prank-msa.SlackBuild | 113 -------------------------------- academic/prank-msa/prank-msa.info | 10 --- academic/prank-msa/slack-desc | 19 ------ 4 files changed, 174 deletions(-) delete mode 100644 academic/prank-msa/README delete mode 100644 academic/prank-msa/prank-msa.SlackBuild delete mode 100644 academic/prank-msa/prank-msa.info delete mode 100644 academic/prank-msa/slack-desc (limited to 'academic') diff --git a/academic/prank-msa/README b/academic/prank-msa/README deleted file mode 100644 index 03d714280f13c..0000000000000 --- a/academic/prank-msa/README +++ /dev/null @@ -1,32 +0,0 @@ -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 deleted file mode 100644 index 0806584320b60..0000000000000 --- a/academic/prank-msa/prank-msa.SlackBuild +++ /dev/null @@ -1,113 +0,0 @@ -#!/bin/bash - -# Slackware build script for prank-msa - -# Copyright 2017-2021 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=$( uname -m ) ;; - esac -fi - -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. -if [ ! -z "${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 deleted file mode 100644 index ab3041d52b35a..0000000000000 --- a/academic/prank-msa/prank-msa.info +++ /dev/null @@ -1,10 +0,0 @@ -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 deleted file mode 100644 index 3a6b88e42b710..0000000000000 --- a/academic/prank-msa/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# 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