academic/kraken: Added (Assigning Taxonomic Labels).

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

5 files changed, 156 insertions, 0 deletions

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: