academic/prank-msa: Removed (ftb + no active maintainer).

Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>

4 files changed, 0 insertions, 174 deletions

diff --git a/academic/prank-msa/README b/academic/prank-msa/README
deleted file mode 100644
index 03d714280f..0000000000
--- 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 0806584320..0000000000
--- 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 ab3041d52b..0000000000
--- 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 3a6b88e42b..0000000000
--- 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: