diff options
Diffstat (limited to 'academic')
-rw-r--r-- | academic/trimmomatic/README | 38 | ||||
-rw-r--r-- | academic/trimmomatic/References | 4 | ||||
-rw-r--r-- | academic/trimmomatic/slack-desc | 19 | ||||
-rw-r--r-- | academic/trimmomatic/trimmomatic.SlackBuild | 67 | ||||
-rw-r--r-- | academic/trimmomatic/trimmomatic.info | 10 |
5 files changed, 138 insertions, 0 deletions
diff --git a/academic/trimmomatic/README b/academic/trimmomatic/README new file mode 100644 index 0000000000..339f90bdea --- /dev/null +++ b/academic/trimmomatic/README @@ -0,0 +1,38 @@ +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 new file mode 100644 index 0000000000..d6aecc31b0 --- /dev/null +++ b/academic/trimmomatic/References @@ -0,0 +1,4 @@ +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 new file mode 100644 index 0000000000..4cf6f99863 --- /dev/null +++ b/academic/trimmomatic/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------------------------------------------------------| +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 0000000000..c419e77b89 --- /dev/null +++ b/academic/trimmomatic/trimmomatic.SlackBuild @@ -0,0 +1,67 @@ +#!/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 new file mode 100644 index 0000000000..b16aab676e --- /dev/null +++ b/academic/trimmomatic/trimmomatic.info @@ -0,0 +1,10 @@ +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" |