mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-16 19:50:19 +01:00
academic/prank-msa: Removed (ftb + no active maintainer).
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>
This commit is contained in:
Matteo Bernardini
Robby Workman
parent
811dac1f48
commit
7a9d94eb69
4 changed files with 0 additions and 174 deletions
|
|
@ -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.
|
||||
|
|
@ -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
|
||||
|
|
@ -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"
|
||||
|
|
@ -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:
|
||||
Loading…
Reference in a new issue