academic/WEVOTE: Added (WEighted VOting Taxonomic idEntification).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
72dd572b55
commit
9c795f8652
|
|
@ -0,0 +1,26 @@
|
|||
WEVOTE (WEighted VOting Taxonomic idEntification)
|
||||
|
||||
WEVOTE is a method that classifies metagenome shotgun sequencing DNA
|
||||
reads based on an ensemble of existing methods using k-mer based,
|
||||
marker-based, and naive-similarity based approaches. The performance
|
||||
evaluation based on fourteen simulated microbiome datasets
|
||||
consistently demonstrates that WEVOTE achieves a high level of
|
||||
sensitivity and precision compared to the individual methods across
|
||||
different taxonomic levels. The major advantage of the WEVOTE pipeline
|
||||
is that the user can make the choice of which tools to use in order to
|
||||
explore the trade-off between sensitivity, precision, time and memory.
|
||||
|
||||
The WEVOTE architecture is flexible so that additional taxonomic tools
|
||||
can be easily added, or the current tools can be replaced by improved
|
||||
ones. Moreover, the score assigned to the taxon for each read
|
||||
indicates the confidence level of the assignment. This information is
|
||||
especially useful for the assessment of false positive annotations at
|
||||
a particular taxonomic level. The classification score given by WEVOTE
|
||||
can be used for any downstream analysis that requires the high
|
||||
confidence of the annotated sequences.
|
||||
|
||||
Publication:
|
||||
Ahmed A. Metwally, Yang Dai, Patricia W. Finn, and David L. Perkins.
|
||||
WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial
|
||||
Sequences.
|
||||
PloS ONE, 2016.
|
||||
|
|
@ -0,0 +1,5 @@
|
|||
Publication:
|
||||
Ahmed A. Metwally, Yang Dai, Patricia W. Finn, and David L. Perkins.
|
||||
WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial
|
||||
Sequences.
|
||||
PloS ONE, 2016.
|
||||
|
|
@ -0,0 +1,105 @@
|
|||
#!/bin/sh
|
||||
|
||||
# Slackware build script for WEVOTE
|
||||
|
||||
# Copyright 2018 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.
|
||||
|
||||
PRGNAM=WEVOTE
|
||||
VERSION=${VERSION:-1.8.0} # The version number is found in "install.sh"
|
||||
COMMIT=645523db5aba843b2681e83146783b18e92866b1
|
||||
BUILD=${BUILD:-1}
|
||||
TAG=${TAG:-_SBo}
|
||||
|
||||
if [ -z "$ARCH" ]; then
|
||||
case "$( uname -m )" in
|
||||
i?86) ARCH=i586 ;;
|
||||
arm*) ARCH=arm ;;
|
||||
*) ARCH=$( uname -m ) ;;
|
||||
esac
|
||||
fi
|
||||
|
||||
CWD=$(pwd)
|
||||
TMP=${TMP:-/tmp/SBo}
|
||||
PKG=$TMP/package-$PRGNAM
|
||||
OUTPUT=${OUTPUT:-/tmp}
|
||||
|
||||
# The -fopenmp compiler flag is required, otherwise the binaries will not build.
|
||||
if [ "$ARCH" = "i586" ]; then
|
||||
SLKCFLAGS="-O2 -march=i586 -mtune=i686 -fopenmp"
|
||||
LIBDIRSUFFIX=""
|
||||
elif [ "$ARCH" = "i686" ]; then
|
||||
SLKCFLAGS="-O2 -march=i686 -mtune=i686 -fopenmp"
|
||||
LIBDIRSUFFIX=""
|
||||
elif [ "$ARCH" = "x86_64" ]; then
|
||||
SLKCFLAGS="-O2 -fPIC -fopenmp"
|
||||
LIBDIRSUFFIX="64"
|
||||
else
|
||||
SLKCFLAGS="-O2 -fopenmp"
|
||||
LIBDIRSUFFIX=""
|
||||
fi
|
||||
|
||||
set -e
|
||||
|
||||
rm -rf $PKG
|
||||
mkdir -p $TMP $PKG $OUTPUT
|
||||
cd $TMP
|
||||
rm -rf $PRGNAM-$COMMIT
|
||||
tar xvf $CWD/$PRGNAM-$COMMIT.tar.gz
|
||||
cd $PRGNAM-$COMMIT
|
||||
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 {} \;
|
||||
|
||||
# Clean up before building
|
||||
make -C src clean
|
||||
make CXXFLAGS="$SLKCFLAGS" -C src
|
||||
install -D -m755 src/$PRGNAM $PKG/usr/bin/$PRGNAM
|
||||
install -D -m755 src/ABUNDANCE $PKG/usr/bin/ABUNDANCE
|
||||
|
||||
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
|
||||
|
||||
# Include the scripts
|
||||
install -D -m755 downloadTaxonomyDB.sh $PKG/usr/include/$PRGNAM/downloadTaxonomyDB.sh
|
||||
install -D -m755 run_ABUNDANCE.sh $PKG/usr/include/$PRGNAM/run_ABUNDANCE.sh
|
||||
install -D -m755 run_STATISTICS.sh $PKG/usr/include/$PRGNAM/run_STATISTICS.sh
|
||||
install -D -m755 run_WEVOTE_PIPELINE.sh $PKG/usr/include/$PRGNAM/run_WEVOTE_PIPELINE.sh
|
||||
install -D -m755 WEVOTE_Statistics.R $PKG/usr/include/$PRGNAM/WEVOTE_Statistics.R
|
||||
|
||||
# Include the file for specifying paths
|
||||
mkdir -p $PKG/usr/share/$PRGNAM
|
||||
cp -a wevote.cfg $PKG/usr/share/$PRGNAM
|
||||
|
||||
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
|
||||
cp -a \
|
||||
LICENSE README.md TUTORIAL.md \
|
||||
$PKG/usr/doc/$PRGNAM-$VERSION
|
||||
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
|
||||
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
|
||||
|
||||
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:-tgz}
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
PRGNAM="WEVOTE"
|
||||
VERSION="1.8.0"
|
||||
HOMEPAGE="https://github.com/aametwally/WEVOTE"
|
||||
DOWNLOAD="https://github.com/aametwally/WEVOTE/archive/645523d/WEVOTE-645523db5aba843b2681e83146783b18e92866b1.tar.gz"
|
||||
MD5SUM="12f96abfa58551fff8d9e09c1cd1a037"
|
||||
DOWNLOAD_x86_64=""
|
||||
MD5SUM_x86_64=""
|
||||
REQUIRES=""
|
||||
MAINTAINER="Petar Petrov"
|
||||
EMAIL="slackalaxy@gmail.com"
|
||||
|
|
@ -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------------------------------------------------------|
|
||||
WEVOTE: WEVOTE (WEighted VOting Taxonomic idEntification)
|
||||
WEVOTE:
|
||||
WEVOTE: WEVOTE is a method that classifies metagenome shotgun sequencing
|
||||
WEVOTE: DNA reads based on an ensemble of existing methods using k-mer
|
||||
WEVOTE: based, marker-based, and naive-similarity based approaches.
|
||||
WEVOTE:
|
||||
WEVOTE: Home: https://github.com/aametwally/WEVOTE/
|
||||
WEVOTE:
|
||||
WEVOTE:
|
||||
WEVOTE:
|
||||
WEVOTE:
|
||||
Loading…
Reference in New Issue