academic/WEVOTE: Added (WEighted VOting Taxonomic idEntification).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

5 files changed, 165 insertions, 0 deletions

diff --git a/academic/WEVOTE/README b/academic/WEVOTE/README
new file mode 100644
index 000000000000..7146dcbd2b63
--- /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 000000000000..f2e026ba41df
--- /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 000000000000..c9090df97931
--- /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 000000000000..3d1eeccdf18d
--- /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 000000000000..b2d97b8332de
--- /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: