From 9c795f86521f125fd759f7f0e7306dfe2303e56a Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Mon, 24 Dec 2018 08:52:55 +0700 Subject: academic/WEVOTE: Added (WEighted VOting Taxonomic idEntification). Signed-off-by: Willy Sudiarto Raharjo --- academic/WEVOTE/README | 26 ++++++++++ academic/WEVOTE/References | 5 ++ academic/WEVOTE/WEVOTE.SlackBuild | 105 ++++++++++++++++++++++++++++++++++++++ academic/WEVOTE/WEVOTE.info | 10 ++++ academic/WEVOTE/slack-desc | 19 +++++++ 5 files changed, 165 insertions(+) create mode 100644 academic/WEVOTE/README create mode 100644 academic/WEVOTE/References create mode 100644 academic/WEVOTE/WEVOTE.SlackBuild create mode 100644 academic/WEVOTE/WEVOTE.info create mode 100644 academic/WEVOTE/slack-desc (limited to 'academic') diff --git a/academic/WEVOTE/README b/academic/WEVOTE/README new file mode 100644 index 0000000000..7146dcbd2b --- /dev/null +++ b/academic/WEVOTE/README @@ -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. diff --git a/academic/WEVOTE/References b/academic/WEVOTE/References new file mode 100644 index 0000000000..f2e026ba41 --- /dev/null +++ b/academic/WEVOTE/References @@ -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. diff --git a/academic/WEVOTE/WEVOTE.SlackBuild b/academic/WEVOTE/WEVOTE.SlackBuild new file mode 100644 index 0000000000..c9090df979 --- /dev/null +++ b/academic/WEVOTE/WEVOTE.SlackBuild @@ -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} diff --git a/academic/WEVOTE/WEVOTE.info b/academic/WEVOTE/WEVOTE.info new file mode 100644 index 0000000000..3d1eeccdf1 --- /dev/null +++ b/academic/WEVOTE/WEVOTE.info @@ -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" diff --git a/academic/WEVOTE/slack-desc b/academic/WEVOTE/slack-desc new file mode 100644 index 0000000000..b2d97b8332 --- /dev/null +++ b/academic/WEVOTE/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------------------------------------------------------| +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: -- cgit v1.2.3