academic/trimmomatic: Added (Trimming Tool).

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

5 files changed, 138 insertions, 0 deletions

diff --git a/academic/trimmomatic/README b/academic/trimmomatic/README
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+Trimmomatic: A flexible read trimming tool for Illumina NGS data
+
+Trimmomatic performs a variety of useful trimming tasks for illumina
+paired-end and single ended data.The selection of trimming steps and
+their associated parameters are supplied on the command line.
+
+The current trimming steps are:
+
+- ILLUMINACLIP: Cut adapter and other illumina-specific sequences from
+  the read.
+- SLIDINGWINDOW: Perform a sliding window trimming, cutting once the
+  average quality within the window falls below a threshold.
+- LEADING: Cut bases off the start of a read, if below a threshold
+  quality
+- TRAILING: Cut bases off the end of a read, if below a threshold
+  quality
+- CROP: Cut the read to a specified length
+- HEADCROP: Cut the specified number of bases from the start of the
+  read
+- MINLEN: Drop the read if it is below a specified length
+- TOPHRED33: Convert quality scores to Phred-33
+- TOPHRED64: Convert quality scores to Phred-64
+
+It works with FASTQ (using phred + 33 or phred + 64 quality scores,
+depending on the Illumina pipeline used), either uncompressed or
+gzipp'ed FASTQ. Use of gzip format is determined based on the .gz
+extension.
+
+For single-ended data, one input and one output file are specified,
+plus the processing steps. For paired-end data, two input files are
+specified, and 4 output files, 2 for the 'paired' output where both
+reads survived the processing, and 2 for corresponding 'unpaired'
+output where a read survived, but the partner read did not.
+
+Citations
+Bolger, A. M., Lohse, M., & Usadel, B. (2014).
+Trimmomatic: A flexible trimmer for Illumina Sequence Data.
+Bioinformatics, btu170.
diff --git a/academic/trimmomatic/References b/academic/trimmomatic/References
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+Citations
+Bolger, A. M., Lohse, M., & Usadel, B. (2014).
+Trimmomatic: A flexible trimmer for Illumina Sequence Data.
+Bioinformatics, btu170.
diff --git a/academic/trimmomatic/slack-desc b/academic/trimmomatic/slack-desc
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+++ b/academic/trimmomatic/slack-desc
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+# 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------------------------------------------------------|
+trimmomatic: trimmomatic (A flexible read trimming tool for Illumina NGS data)
+trimmomatic:
+trimmomatic: Trimmomatic performs a variety of useful trimming tasks for illumina
+trimmomatic: paired-end and single ended data.The selection of trimming steps and
+trimmomatic: their associated parameters are supplied on the command line.
+trimmomatic:
+trimmomatic: Home: http://www.usadellab.org/cms/?page=trimmomatic
+trimmomatic:
+trimmomatic:
+trimmomatic:
+trimmomatic:
diff --git a/academic/trimmomatic/trimmomatic.SlackBuild b/academic/trimmomatic/trimmomatic.SlackBuild
new file mode 100644
index 0000000000000..c419e77b89053
--- /dev/null
+++ b/academic/trimmomatic/trimmomatic.SlackBuild
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+#!/bin/sh
+
+# Slackware build script for trimmomatic
+
+# Copyright trimmomatic 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=trimmomatic
+ZIPNAM=Trimmomatic
+VERSION=${VERSION:-0.38}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+ARCH=noarch
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}	# For consistency's sake, use this
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}	# Drop the package in /tmp
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $ZIPNAM-$VERSION
+unzip $CWD/$ZIPNAM-$VERSION.zip
+cd $ZIPNAM-$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 {} \;
+
+install -D -m755 $PRGNAM-$VERSION.jar $PKG/usr/bin/$PRGNAM.jar
+
+mkdir -p $PKG/usr/share/$PRGNAM
+cp -a adapters $PKG/usr/share/$PRGNAM
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a LICENSE $PKG/usr/doc/$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/trimmomatic/trimmomatic.info b/academic/trimmomatic/trimmomatic.info
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+PRGNAM="trimmomatic"
+VERSION="0.38"
+HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"
+DOWNLOAD="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip"
+MD5SUM="4b3df3caf7fe803ca54c79db1a99c464"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES="jdk"
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmailc.com"