From ce35e022abf5bd0b53656f777a3d668b6579f000 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Tue, 25 Dec 2018 05:38:56 +0700 Subject: [PATCH] academic/kraken: Added (Assigning Taxonomic Labels). Signed-off-by: Willy Sudiarto Raharjo --- academic/kraken/README | 21 +++++++ academic/kraken/References | 5 ++ academic/kraken/kraken.SlackBuild | 101 ++++++++++++++++++++++++++++++ academic/kraken/kraken.info | 10 +++ academic/kraken/slack-desc | 19 ++++++ 5 files changed, 156 insertions(+) create mode 100644 academic/kraken/README create mode 100644 academic/kraken/References create mode 100644 academic/kraken/kraken.SlackBuild create mode 100644 academic/kraken/kraken.info create mode 100644 academic/kraken/slack-desc diff --git a/academic/kraken/README b/academic/kraken/README new file mode 100644 index 0000000000..21eaa3ad87 --- /dev/null +++ b/academic/kraken/README @@ -0,0 +1,21 @@ +Kraken is a system for assigning taxonomic labels to short DNA +sequences, usually obtained through metagenomic studies. Previous +attempts by other bioinformatics software to accomplish this task have +often used sequence alignment or machine learning techniques that were +quite slow, leading to the development of less sensitive but much faster +abundance estimation programs. Kraken aims to achieve high sensitivity +and high speed by utilizing exact alignments of k-mers and a novel +classification algorithm. + +In its fastest mode of operation, for a simulated metagenome of 100 bp +reads, Kraken processed over 4 million reads per minute on a single +core, over 900 times faster than Megablast and over 11 times faster than +the abundance estimation program MetaPhlAn. Kraken's accuracy is +comparable with Megablast, with slightly lower sensitivity and very high +precision. + +REFERENCE +Wood DE, Salzberg SL +Kraken: ultrafast metagenomic sequence classification using exact +alignments. +Genome Biology 2014, 15:R46. diff --git a/academic/kraken/References b/academic/kraken/References new file mode 100644 index 0000000000..90d00d30fd --- /dev/null +++ b/academic/kraken/References @@ -0,0 +1,5 @@ +REFERENCE +Wood DE, Salzberg SL +Kraken: ultrafast metagenomic sequence classification using exact +alignments. +Genome Biology 2014, 15:R46. diff --git a/academic/kraken/kraken.SlackBuild b/academic/kraken/kraken.SlackBuild new file mode 100644 index 0000000000..5b1eacebcb --- /dev/null +++ b/academic/kraken/kraken.SlackBuild @@ -0,0 +1,101 @@ +#!/bin/sh + +# Slackware build script for kraken + +# 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=kraken +VERSION=${VERSION:-1.1} +BUILD=${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=${OUTPUT:-/tmp} + +if [ "$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 $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$VERSION +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 {} \; + +mkdir -p $PKG/usr/bin + +sed -i "s:\$(KRAKEN_DIR):$PKG/usr/bin:g" src/Makefile +make CXXFLAGS="$SLKCFLAGS" -C src install + +# Set Kraken path +sed -i "s:#####=KRAKEN_DIR=#####:/usr/bin:g" scripts/kraken scripts/kraken-* +sed -i "s:#####=VERSION=####:${VERSION}:g" scripts/kraken scripts/kraken-* + +# Install the scripts in /usr/bin +# Maybe another place will be better? +cd scripts +for script in * ; do + install -D -m755 $script $PKG/usr/bin/$script +done +cd .. + +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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a CHANGELOG LICENSE README.md docs/MANUAL.markdown $PKG/usr/doc/$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/kraken/kraken.info b/academic/kraken/kraken.info new file mode 100644 index 0000000000..7b78c71755 --- /dev/null +++ b/academic/kraken/kraken.info @@ -0,0 +1,10 @@ +PRGNAM="kraken" +VERSION="1.1" +HOMEPAGE="http://ccb.jhu.edu/software/kraken/" +DOWNLOAD="https://github.com/DerrickWood/kraken/archive/v1.1/kraken-1.1.tar.gz" +MD5SUM="da11f520b3ff21228ac0ceff5ad895a4" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="jellyfish_k-mer" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/kraken/slack-desc b/academic/kraken/slack-desc new file mode 100644 index 0000000000..d394ce6fb6 --- /dev/null +++ b/academic/kraken/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------------------------------------------------------| +kraken: kraken (Assign taxonomic labels to short DNA sequences) +kraken: +kraken: Kraken is a system for assigning taxonomic labels to short DNA +kraken: sequences, usually obtained through metagenomic studies. Kraken +kraken: aims to achieve high sensitivity and high speed by utilizing exact +kraken: alignments of k-mers and a novel classification algorithm. +kraken: +kraken: Home: http://ccb.jhu.edu/software/kraken/ +kraken: +kraken: +kraken: