debian/0000755000000000000000000000000012153653622007173 5ustar debian/source/0000755000000000000000000000000012153653434010474 5ustar debian/source/format0000644000000000000000000000001412153653434011702 0ustar 3.0 (quilt) debian/fastqc.10000644000000000000000000000754412153653615010552 0ustar .TH FASTQC "1" "November 2012" "FastQC v0.10.1" "User Commands" .SH NAME FastQC \- high throughput sequence QC analysis tool .PP SYNOPSIS .IP fastqc seqfile1 seqfile2 .. seqfileN .IP fastqc [\-o output dir] [\-\-(no)extract] [\-f fastq|bam|sam] .IP [\-c contaminant file] seqfile1 .. seqfileN .PP .SH DESCRIPTION .IP FastQC reads a set of sequence files and produces from each one a quality control report consisting of a number of different modules, each one of which will help to identify a different potential type of problem in your data. .IP If no files to process are specified on the command line then the program will start as an interactive graphical application. If files are provided on the command line then the program will run with no user interaction required. In this mode it is suitable for inclusion into a standardised analysis pipeline. .IP The options for the program as as follows: .TP \fB\-h\fR \fB\-\-help\fR Print this help file and exit .TP \fB\-v\fR \fB\-\-version\fR Print the version of the program and exit .TP \fB\-o\fR \fB\-\-outdir\fR Create all output files in the specified output directory. Please note that this directory must exist as the program will not create it. If this option is not set then the output file for each sequence file is created in the same directory as the sequence file which was processed. .TP \fB\-\-casava\fR Files come from raw casava output. Files in the same sample group (differing only by the group number) will be analysed as a set rather than individually. Sequences with the filter flag set in the header will be excluded from the analysis. Files must have the same names given to them by casava (including being gzipped and ending with .gz) otherwise they won't be grouped together correctly. .TP \fB\-\-extract\fR If set then the zipped output file will be uncompressed in the same directory after it has been created. By default this option will be set if fastqc is run in non\-interactive mode. .TP \fB\-j\fR \fB\-\-java\fR Provides the full path to the java binary you want to use to launch fastqc. If not supplied then java is assumed to be in your path. .TP \fB\-\-noextract\fR Do not uncompress the output file after creating it. You should set this option if you do not wish to uncompress the output when running in non\-interactive mode. .TP \fB\-\-nogroup\fR Disable grouping of bases for reads >50bp. All reports will show data for every base in the read. WARNING: Using this option will cause fastqc to crash and burn if you use it on really long reads, and your plots may end up a ridiculous size. You have been warned! .TP \fB\-f\fR \fB\-\-format\fR Bypasses the normal sequence file format detection and forces the program to use the specified format. Valid formats are bam,sam,bam_mapped,sam_mapped and fastq .TP \fB\-t\fR \fB\-\-threads\fR Specifies the number of files which can be processed simultaneously. Each thread will be allocated 250MB of memory so you shouldn't run more threads than your available memory will cope with, and not more than 6 threads on a 32 bit machine .TP \fB\-c\fR Specifies a non\-default file which contains the list of .TP \fB\-\-contaminants\fR contaminants to screen overrepresented sequences against. The file must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored. .TP \fB\-k\fR \fB\-\-kmers\fR Specifies the length of Kmer to look for in the Kmer content module. Specified Kmer length must be between 2 and 10. Default length is 5 if not specified. .TP \fB\-q\fR \fB\-\-quiet\fR Supress all progress messages on stdout and only report errors. .PP .SH BUGS .IP Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk or in www.bioinformatics.babraham.ac.uk/bugzilla/ .SH AUTHOR .IP This manpage was created using \fBhelp2man\fR by Andreas Tille for the Debian distribution but can be used by others as well. debian/copyright0000644000000000000000000000215712153653615011135 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: FastQC Source: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Files-Excluded: *.jar Files: * Copyright: Simon Adrews License: GPL-3.0+ Files: debian/* Copyright: 2012 Steffen Moeller License: GPL-3.0+ License: GPL-3.0+ 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 package 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 . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". debian/compat0000644000000000000000000000000212153653615010373 0ustar 9 debian/README.source0000644000000000000000000000051312153653615011353 0ustar fastqc for Debian ----------------- By using a not yet released version of uscan from Git git://tille@git.debian.org/git/users/tille/devscripts.git the following changes to the upstream tarball were approached: 1. Removal of .jar files fastqc-*/jbzip2-0.9.jar fastqc-*/sam-1.32.jar 2. Removal of all .svn directories debian/watch0000644000000000000000000000022412153653615010224 0ustar version=3 opts="dversionmangle=s/\+dfsg//g" \ http://www.bioinformatics.babraham.ac.uk/projects/download.html fastqc/fastqc_v([.\d]+)_source\.zip debian/docs0000644000000000000000000000003512153653615010046 0ustar README.txt RELEASE_NOTES.txt debian/patches/0000755000000000000000000000000012153653434010623 5ustar debian/patches/series0000644000000000000000000000010112153653434012030 0ustar Makefile.patch fastqc.patch fix-help-call.patch fix_icon_loading debian/patches/Makefile.patch0000644000000000000000000000135712153653434013367 0ustar From: Steffen Moeller Subject: Simplyfy installation by creating a Makefile --- /dev/null +++ b/Makefile @@ -0,0 +1,19 @@ + +all: fastqc.jar + +fastqc.jar: + javac -cp /usr/share/java/sam.jar:/usr/share/java/jbzip2.jar `find uk -name "*.java"` + jar cf fastqc.jar `find uk -name "*.class" -o -name "*.png"` + +DESTDIR= +PREFIX=/usr +install: fastqc.jar + mkdir -p $(DESTDIR)$(PREFIX)/bin/ + cp -a fastqc $(DESTDIR)$(PREFIX)/bin/ + chmod +x $(DESTDIR)$(PREFIX)/bin/fastqc + mkdir -p $(DESTDIR)$(PREFIX)/share/fastqc/ + cp -a fastqc.jar $(DESTDIR)$(PREFIX)/share/fastqc/ + cp -r Contaminants Templates Help $(DESTDIR)$(PREFIX)/share/fastqc/ + +clean: + find . -name "*.jar" -o -name "*.class" | xargs -r rm + +.PHONY: all install debian/patches/fix_icon_loading0000644000000000000000000000465612153653434014054 0ustar Subject: issue when loading resources Description: in Debian, templates and other resources are not embedded in Jar file. This is a problem when app tries to access the resources. This patch provides the path in Debian hierarcy to find resources. Author: Olivier Sallou Last-Updated: 2013-06-05 Forwarded: no --- a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java +++ b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java @@ -167,12 +167,12 @@ data.append("\n"); // Add in the icon files for pass/fail/warn - File templatesDir = new File(URLDecoder.decode(ClassLoader.getSystemResource("Templates/Icons").getFile(),"UTF-8")); + File templatesDir = new File("/usr/share/fastqc/Templates/Icons"); String [] names = templatesDir.list(); for (int n=0;n 0) { zip.write(buffer, 0, len); @@ -235,7 +235,7 @@ private void addTemplate (String filename, String date) throws IOException { - BufferedReader br = new BufferedReader(new FileReader(new File(URLDecoder.decode(ClassLoader.getSystemResource("Templates/header_template.html").getFile(),"UTF-8")))); + BufferedReader br = new BufferedReader(new FileReader(new File("/usr/share/fastqc/Templates/header_template.html"))); String line; while ((line = br.readLine())!=null) { --- a/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java +++ b/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java @@ -60,7 +60,7 @@ try { - File contaminantFile = new File (URLDecoder.decode(ClassLoader.getSystemResource("Contaminants/contaminant_list.txt").getFile(),"UTF-8")); + File contaminantFile = new File ("/usr/share/fastqc/Contaminants/contaminant_list.txt"); if (System.getProperty("fastqc.contaminant_file") != null && System.getProperty("fastqc.contaminant_file").length()>0) { contaminantFile = new File(System.getProperty("fastqc.contaminant_file")); debian/patches/fix-help-call.patch0000644000000000000000000000152112153653434014270 0ustar From: Andreas Tille Subject: The original way to open Help text ends up in an exception Setting the explicite file name as well as avoiding the call to ClassLoader.getSystemResource helps fixing this. Specifically the later is important, see https://lists.debian.org/debian-med/2012/11/msg00073.html --- a/uk/ac/babraham/FastQC/FastQCMenuBar.java +++ b/uk/ac/babraham/FastQC/FastQCMenuBar.java @@ -132,7 +132,7 @@ public class FastQCMenuBar extends JMenu } else if (command.equals("help_contents")) { try { - new HelpDialog(application,new File(URLDecoder.decode(ClassLoader.getSystemResource("Help").getFile(),"UTF-8"))); + new HelpDialog(application,new File(URLDecoder.decode("/usr/share/fastqc/Help","UTF-8"))); } catch (UnsupportedEncodingException e1) { e1.printStackTrace(); debian/patches/fastqc.patch0000644000000000000000000000236012153653434013126 0ustar From: Steffen Moeller Subject: Ensure proper CLASSPATH according to location of Debian JARs --- a/fastqc +++ b/fastqc @@ -17,12 +17,12 @@ $delimiter = ';'; } +my $JavaClasspathExtraDir="/usr/share/java"; + if ($ENV{CLASSPATH}) { - $ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/sam-1.32.jar$delimiter$RealBin/jbzip2-0.9.jar"; -} -else { - $ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/sam-1.32.jar$delimiter$RealBin/jbzip2-0.9.jar"; + $ENV{CLASSPATH} .= "$delimiter"; } +$ENV{CLASSPATH} .= "$JavaClasspathExtraDir/sam.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar:$RealBin/fastqc.jar"; my @java_args; my @files; @@ -177,10 +177,10 @@ if ($java_bin ne 'java') { - system $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication", @files; + system $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar", @files; } else { - exec $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication", @files; + exec $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar", @files; } __DATA__ @@ -273,4 +273,4 @@ Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk or in www.bioinformatics.babraham.ac.uk/bugzilla/ - \ No newline at end of file + debian/README.Debian0000644000000000000000000000636212153653615011245 0ustar fastqc for Debian ----------------- You can run FastQC in one of two modes, either as an interactive graphical application in which you can dynamically load FastQ files and view their results. Alternatively you can run FastQC in a non-interactive mode where you specify the files you want to process on the command line and FastQC will generate an HTML report for each file without launching a user interface. This would allow FastQC to be run as part of an analysis pipeline. Running FastQC Interactively ---------------------------- A wrapper is installed into /usr/bin/fastqc Running FastQC as part of a pipeline ------------------------------------ To run FastQC non-interactively you should use the fastqc wrapper script to launch the program. To run non-interactively you simply have to specify a list of files to process on the commandline fastqc somefile.txt someotherfile.txt You can specify as many files to process in a single run as you like. If you don't specify any files to process the program will try to open the interactive application which may result in an error if you're running in a non-graphical environment. There are a few extra options you can specify when running non-interactively. Full details of these can be found by running fastqc --help By default, in non-interactive mode FastQC will create both a zipped copy of the QC report, and also extract this to create a folder which contains the report files ready to be viewed. If you only want to create the zipped file then you can add --noextract To the launch command to suppress the unzipping. If you want to save your reports in a folder other than the folder which contained your original FastQ files then you can specify an alternative location by setting a --outdir value: --outdir=/some/other/dir/ Customising the report output ----------------------------- If you want to run FastQC as part of a sequencing pipeline you may wish to change the formatting of the report to add in your own branding or to include extra information. In the Templates directory you will find a file called 'header_template.html' which you can edit to change the look of the report. This file contains all of the header for the report file, including the CSS section and you can alter this however you see fit. If you want to add in your own logo or other image files to the reports then you can drop a png or jpg file into the Icons folder in the templates directory and this will be copied into the report folder for all reports generated by the program. You can refer to these icons using a relative URL (eg Icons/image.png) in the HTML template. Images placed outside the icons directory will not be copied. Whilst you can make whatever changes you like you should probably leave in place the
structure of the html template since later code will expect to close the main div which is left open at the end of the header. There is no facility to change the code in the main body of the report or the footer (although you can of course change the styling). The text tags @@FILENAME@@ and @@DATE@@ are placeholders which are filled in when the report it created. You can use these placeholders in other parts of the header if you wish. -- Andreas Tille Wed, 07 Nov 2012 14:24:25 +0100 debian/menu0000644000000000000000000000016012153653615010061 0ustar ?package(fastqc):needs="X11" section="Applications/Science/Biology"\ title="fastqc" command="/usr/bin/fastqc" debian/manpages0000644000000000000000000000001312153653615010705 0ustar debian/*.1 debian/control0000644000000000000000000000277512153653615010613 0ustar Source: fastqc Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Olivier Sallou Build-Depends: debhelper (>= 9), javahelper, default-jdk, libsam-java, libjbzip2-java Standards-Version: 3.9.4 Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Vcs-Svn: http://svn.debian.org/debian-med/trunk/packages/babraham/fastqc/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/babraham/fastqc/trunk/ Package: fastqc Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, libsam-java, libjbzip2-java Description: quality control for high throughput sequence data FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. . The main functions of FastQC are * Import of data from BAM, SAM or FastQ files (any variant) * Providing a quick overview to tell you in which areas there may be problems * Summary graphs and tables to quickly assess your data * Export of results to an HTML based permanent report * Offline operation to allow automated generation of reports without running the interactive application debian/rules0000755000000000000000000000111512153653615010253 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ --with javahelper get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --repack --destdir ../tarballs # Alternatively you might like to use the following uscan command # that requires devscripts > 2.12.4 which is not yet released at # the time writing. The code can be obtained via # git clone git://tille@git.debian.org/git/users/tille/devscripts.git # and then use scripts/uscan.pl # uscan --verbose --force-download --repack-compression xz --destdir ../tarballs debian/upstream0000644000000000000000000000014712153653615010762 0ustar Name: FastQC Contact: simon.andrews@babraham.ac.uk Gallery: http://www.youtube.com/user/BabrahamBioinf debian/changelog0000644000000000000000000000057312153653615011054 0ustar fastqc (0.10.1+dfsg-2) unstable; urgency=low * Add patch to fix Templates and Contaminants loading in non interactive mode (Closes: #697604) -- Olivier Sallou Wed, 05 Jun 2013 17:08:44 +0200 fastqc (0.10.1+dfsg-1) unstable; urgency=low * Initial release (Closes: #670353) -- Andreas Tille Tue, 20 Nov 2012 13:38:32 +0100 debian/manifest0000644000000000000000000000022312153653615010723 0ustar /usr/share/fastqc/fastqc.jar: Main-Class: uk.ac.babraham.FastQC.FastQCApplication Class-Path: /usr/share/java/jbzip2.jar /usr/share/java/sam.jar