debian/0000755000000000000000000000000012265016316007170 5ustar debian/TrimmomaticPE.10000644000000000000000000000742212214301021011751 0ustar .TH "TRIMMOMATICPE" "1" "July 2012" "Trimmomatic 0.22" "Trimmomatic Manual" .SH "NAME" TrimmomaticPE \- flexible read trimming tool for Illumina NGS data .SH "SYNOPSIS" Paired End Mode: .P \fBTrimmomaticPE\fR [\-threads \fIthreads\fR] [\-phred33 | \-phred64] [\-trimlog \fIlogFile\fR] \fIpaired output 1\fR \fIunpaired output 1\fR \fIpaired output 2\fR \fIunpaired output 2\fR \fIstep 1\fR \.\.\. .P Single End Mode: .P \fBTrimmomaticSE\fR [\-threads \fIthreads\fR] [\-phred33 | \-phred64] [\-trimlog \fIlogFile\fR] \fIoutput\fR \fIstep 1\fR \.\.\. .SH "DESCRIPTION" 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. .SH "OPTIONS" .PP \fB\-phred\fR .RS 4 If no quality score is specified, phred\-64 is the default. .RE .PP \fB\-trimlog\fR .RS 4 Specifying a trimlog file creates a log of all read trimmings, indicating the following details: .IP "\(bu" 4 the read name .IP "\(bu" 4 the surviving sequence length .IP "\(bu" 4 the location of the first surviving base, aka\. the amount trimmed from the start .IP "\(bu" 4 the location of the last surviving base in the original read .IP "\(bu" 4 the amount trimmed from the end .IP "" 0 Multiple steps can be specified as required, by using additional arguments at the end\. . .P Most steps take one or more settings, delimited by \':\' (a colon) . .P Step options: . .IP "" 4 . .nf ILLUMINACLIP:::: fastaWithAdaptersEtc: specifies the path to a fasta file containing all the adapters, PCR sequences etc\. The naming of the various sequences within this file determines how they are used\. See below\. seedMismatches: specifies the maximum mismatch count which will still allow a full match to be performed palindromeClipThreshold: specifies how accurate the match between the two \'adapter ligated\' reads must be for PE palindrome read alignment\. simpleClipThreshold: specifies how accurate the match between any adapter etc\. sequence must be against a read\. SLIDINGWINDOW:: windowSize: specifies the number of bases to average across requiredQuality: specifies the average quality required\. LEADING: quality: Specifies the minimum quality required to keep a base\. TRAILING: quality: Specifies the minimum quality required to keep a base\. CROP: length: The number of bases to keep, from the start of the read\. HEADCROP: length: The number of bases to remove from the start of the read\. MINLENGTH: length: Specifies the minimum length of reads to be kept\. .fi . .IP "" 0 . .P Trimming Order .P Trimming occurs in the order which the steps are specified on the command line\. It is recommended in most cases that adapter clipping, if required, is done as early as possible\. .SH "EXAMPLES" Paired End: .P \fBTrimmomaticPE\fR s_1_1_sequence\.txt\.gz s_1_2_sequence\.txt\.gz lane1_forward_paired\.fq\.gz lane1_forward_unpaired\.fq\.gz lane1_reverse_paired\.fq\.gz lane1_reverse_unpaired\.fq\.gz ILLUMINACLIP:illuminaClipping\.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 . .P This will perform the following: .IP "" 4 .nf Remove adapters Remove leading low quality or N bases (below quality 3) Remove trailing low quality or N bases (below quality 3) Scan the read with a 4\-base wide sliding window, cutting when the average quality per base drops below 15 Drop reads below the 36 bases long .fi . .IP "" 0 . .P The equivalent for single\-ended reads is: .P \fBTrimmomaticSE\fR s_1_1_sequence\.txt\.gz lane1_forward\.fq\.gz ILLUMINACLIP:illuminaClipping\.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 debian/control0000644000000000000000000000365312265016154010602 0ustar Source: trimmomatic Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Steffen Moeller Section: science Priority: optional Build-Depends: debhelper (>= 9), default-jdk | openjdk-7-jdk, javahelper, ant, libjbzip2-java Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/trimmomatic/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/trimmomatic/trunk/ Homepage: http://www.usadellab.org/cms/index.php?page=trimmomatic Package: trimmomatic Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, libjbzip2-java, default-jre Description: 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 thes 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 * MINLENGTH: 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. debian/install0000644000000000000000000000002512214301021010536 0ustar debian/bin/* usr/bin debian/bin/0000755000000000000000000000000012214301021007720 5ustar debian/bin/TrimmomaticPE0000644000000000000000000000046412214301021012361 0ustar #!/bin/sh PKGNAME=trimmomatic FUNCNAME=`basename $0` JARDIR=/usr/share/java JARVERSION=`ls $JARDIR/$PKGNAME-*.jar | sort | tail -n 1` if [ "" = "$JARVERSION" ] ; then echo "Broken installation of $PKGNAME. JAR not found." exit 1 fi java -classpath "$JARVERSION" org.usadellab.$PKGNAME.$FUNCNAME $@ debian/MANIFEST.MF0000644000000000000000000000023712214301021010604 0ustar Manifest-Version: 1.0 Created-By: Olivier Sallou Main-Class: org.usadellab.trimmomatic.Trimmomatic Class-Path: /usr/share/java/jbzip2.jar debian/rules0000755000000000000000000000137612214301021010237 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules file for trimmomatic # Andreas Tille # GPL pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') ver := $(shell dpkg-parsechangelog | awk '/^Version/ { print $$2 }' | cut -d- -f1 ) %: dh $@ --with javahelper override_dh_auto_build: cp debian/MANIFEST.MF . if [ ! -d dist/unpack ]; then mkdir -p dist/unpack; fi touch dist/unpack/LICENCE touch dist/unpack/AUTHORS ant override_dh_clean: rm -f MANIFEST.MF dh_clean #override_dh_link: # dh_link # # enable symlinking without any need to edit for new versions # dh_link usr/share/java/$(pkg)-$(ver).jar usr/share/java/$(pkg).jar get-orig-source: # uscan --verbose --force-download --repack --rename . debian/get-orig-source debian/trimmomatic.links0000644000000000000000000000017112214301021012536 0ustar usr/bin/TrimmomaticPE usr/bin/TrimmomaticSE usr/share/man/man1/TrimmomaticPE.1.gz usr/share/man/man1/TrimmomaticSE.1.gzdebian/manpages0000644000000000000000000000001312214301021010660 0ustar debian/*.1 debian/watch0000644000000000000000000000031312214301021010176 0ustar version=3 opts=dversionmangle=s/[~\+]dfsg// \ http://www.usadellab.org/cms/index.php?page=trimmomatic \ uploads/supplementary/Trimmomatic/Trimmomatic-Src-([.\d]*).zip \ debian debian/get-orig-source debian/copyright0000644000000000000000000000262612214301021011111 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Trimmomatic Upstream-Contact: Federico Giorgi , Anthony Bolger Source: http://www.usadellab.org/cms/index.php?page=trimmomatic Files-Excluded: lib/*.jar old Files: * Copyright: © 2009-2011 Bjoern Usadel , Anthony Bolger © 2011-2013 Federico Giorgi License: GPL-3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . Comment: On Debian systems, the complete text of the GNU General Public License version 3 can be found in /usr/share/common-licenses/GPL-3. Files: debian/* Copyright: © 2011, Andreas Tille License: GPL-3+ Same as package itself debian/source/0000755000000000000000000000000012214301021010450 5ustar debian/source/format0000644000000000000000000000001412214301021011656 0ustar 3.0 (quilt) debian/get-orig-source0000755000000000000000000000041212265016051012122 0ustar #!/bin/sh # get source for trimmomatic and delete *.JARs from it if uscan --help | grep -q -- --repack-compression ; then echo "Use new enhanced uscan" uscan --verbose --force-download --repack-compression xz exit fi uscan --verbose --force-download debian/changelog0000644000000000000000000000205712265016316011046 0ustar trimmomatic (0.32+dfsg-1) unstable; urgency=low * debian/copyright: Fix contact and copyright * debian/get-orig-source: Trust new uscan to create clean upstream source tarball * debian/control: cme fix dpkg-control -- Andreas Tille Mon, 13 Jan 2014 18:00:20 +0100 trimmomatic (0.30+dfsg-1) unstable; urgency=low * New upstream version * debian/copyright: - DEP5 - Add Files-Excluded to document what was removed from original source * debian/watch: handle +dfsg suffix * debian/get-orig-source: use new uscan if available * debian/control: - cme fix dpkg-control - debhelper 9 - use anonscm in Vcs fields - Build-Depends: default-jdk | ... Closes: #718850 [ Olivier Sallou] * Manage java libs with javahelper * Provide upstream missing MANIFEST.MF -- Andreas Tille Wed, 07 Aug 2013 12:14:33 +0200 trimmomatic (0.22-1) unstable; urgency=low * Initial release (Closes: #682213). -- Andreas Tille Wed, 25 Jul 2012 16:34:43 +0200 debian/trimmomatic.jlibs0000644000000000000000000000003112214301021012514 0ustar dist/jar/trimmomatic.jar debian/patches/0000755000000000000000000000000012265017454010623 5ustar debian/patches/remove_jar_version.path0000644000000000000000000000112612214301021015353 0ustar Author: Olivier Sallou Subject: remove version in generated jar Description: remove version to manage jar file with javahelper Forwarded: no Last-Updated: 2013-08-08 --- a/build.xml +++ b/build.xml @@ -63,7 +63,7 @@ - + debian/patches/there_is_no_MANIFEST.MF.patch0000644000000000000000000000130012214301021015677 0ustar Author: Andreas Tille Description: Try to cure the build failure BUILD FAILED $(CURDIR)/build.xml:66: Manifest file: /tmp/buildd/trimmomatic-0.30+dfsg/MANIFEST.MF does not exist. . This does not really help to finally build the package. Is the file just lacking from upstream? --- a/build.xml +++ b/build.xml @@ -63,7 +63,7 @@ - + debian/patches/series0000644000000000000000000000005512214301021012014 0ustar buildxmlJbzip2.patch remove_jar_version.path debian/patches/buildxmlJbzip2.patch0000644000000000000000000000111412265017454014542 0ustar Author: Andreas Tille Description: Use Debian packaged bzip2 library --- a/build.xml +++ b/build.xml @@ -2,7 +2,7 @@ - + @@ -25,7 +25,7 @@ - + debian/compat0000644000000000000000000000000212214301021010346 0ustar 9 debian/manifest0000644000000000000000000000011112214301021010672 0ustar /usr/share/java/trimmomatic.jar: Class-Path: /usr/share/java/jbzip2.jar