[simonandrews]

One problem did arise:

Failed to process -Dfastqc.output_dir=./fastqc/ :fastqc doesn't exist

I think you're constructing your command incorrectly. The error says that it's treating the -Dfastqc.output_dir... as a file to process rather than a command line argument.

The structure of the command needs to be:

java [options] [class] [files]

..and I suspect you're doing:

java [class] [options] [files]

So you need something like:

java -Xmx1024m -cp /usr/local/FastQC:$CLASSPATH -Dfastqc.output_dir=/output/dir uk.ac.bbsrc.babraham.FastQC.FastQCApplication file1.fastq file2.fastq

Hope this helps

[Bruins]

Hi,

Yes, that helps. Silly of me, I did:

java -Xmx250m -cp ~/bin/FastQC:$CLASSPATH uk.ac.bbsrc.babraham.FastQC.FastQCApplication s_1_1_sequence.txt -Dfastqc.output_dir=fastqc/

that obviously doesn't work...

Wil

[mard]

It's a bug in the templating system. There's a check which should stop anything other than image files getting added to the template, but looking again I see that it's not being applied correctly.

I'll put out an update which fixes this, but the temporary work round is to go into the Templates directory and do:

rm -r .svn

..which should fix the problem in the current version.

Sorry about that.

Simon.

That fixed it. Thanks for that!

[simonandrews]

FastQC v0.3.1

I've just put FastQC v0.3.1 up on our website. This fixes the problem with invalid template files crashing the program. It also fixes a bug with the reporting of progress in the non-interactive version of the program and adds in some missing documentation.

You can get the new version from:

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

[If you don't see the new version of any page hit control+refresh to force our cache to update]

[NGSfan]

this may sound whiny, but does anyone have any tips on how to make an alias or some sort of command line short cut to call FastQC ? some of us have carpel tunnel

for example convert this:

java -Xmx250m -classpath /Tools/FastQC/ uk.ac.bbsrc.babraham.FastQC.FastQCApplication

to something simple like:

fastqc

[simonandrews]

Try saving the following into the FastQC install directory under the name 'fastqc':

#!/usr/bin/perl
use warnings;
use strict;
use FindBin qw($Bin);


if ($ENV{CLASSPATH}) {
        $ENV{CLASSPATH} .= $Bin;
}
else {
        $ENV{CLASSPATH} = $Bin;
}

exec "java", "-Xmx250m", "uk.ac.bbsrc.babraham.FastQC.FastQCApplication", @ARGV;

It's a bit limited in that you can't set any extra java options, but once you make this executable then you should be able to execute this file directly to launch the program.

[Bruins]

For a moment there I tricked myself into recommending adding an alias to your bashrc. A handy solution for command you execute regularly. Open ~/.bashrc (mind the dot!) or create the file. I'm not sure whether this is required but my .bashrc starts with:

if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

this is to source the global defenitions.
Now add your own aliases at the bottom, like so:

alias la='ls -la'
alias ni='ssh -Y [email protected]'

etcetera.

But you have to supply additional arguments which are different each time you call FastQC. So you could create a small shell script to do the work. Let me try something, I'll get back here in a moment.

<snip>

[NGSfan]

Try saving the following into the FastQC install directory under the name 'fastqc':

#!/usr/bin/perl
use warnings;
use strict;
use FindBin qw($Bin);


if ($ENV{CLASSPATH}) {
        $ENV{CLASSPATH} .= $Bin;
}
else {
        $ENV{CLASSPATH} = $Bin;
}

exec "java", "-Xmx250m", "uk.ac.bbsrc.babraham.FastQC.FastQCApplication", @ARGV;

It's a bit limited in that you can't set any extra java options, but once you make this executable then you should be able to execute this file directly to launch the program.

This perl script worked for me! very nice indeed! thank you very much!

[NGSfan]

For a moment there I tricked myself into recommending adding an alias to your bashrc. A handy solution for command you execute regularly. Open ~/.bashrc (mind the dot!) or create the file. I'm not sure whether this is required but my .bashrc starts with:

if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

this is to source the global defenitions.
Now add your own aliases at the bottom, like so:

alias la='ls -la'
alias ni='ssh -Y [email protected]'

etcetera.

But you have to supply additional arguments which are different each time you call FastQC. So you could create a small shell script to do the work. Let me try something, I'll get back here in a moment.

<snip>

yes for passing on additional arguments, then perhaps sticking to the perl script script is a solution. I wouldn't bother too much with the alias approach - the perl script does the job.

Very cool way of doing it I must say.

[simonandrews]

This perl script worked for me! very nice indeed! thank you very much!

But it also had a bug in it :-)

This version should work on all systems (if they have perl installed), and will let you set both java arguments and pass in files as arguments. I may add it to the next release.

#!/usr/bin/perl
use warnings;
use strict;
use FindBin qw($Bin);


if ($ENV{CLASSPATH}) {
	$ENV{CLASSPATH} .= ":$Bin";
}
else {
	$ENV{CLASSPATH} = $Bin;
}

my @java_args = '-Xmx250m';
my @files;

foreach (@ARGV) {
  if (/^\-/) {
    push @java_args,$_;
  }
  else {
    push @files,$_;
  }
}


exec "java",@java_args, "uk.ac.bbsrc.babraham.FastQC.FastQCApplication", @files;

[Bruins]

</snip>

And suddenly posts appeared... I'll need to use f5 more... My shell-script would have been similar to Simon's perl. No alias if you wish to pass arguments. Stick with the perl.

Wil

ps Simon thank you for all your very quick replies!

[ScottC]

I'd be interested in seeing some reports from other people's runs. I'm always keen to compare our instrument's data output, even in a very summarised format such as this, with other instruments around the world. Is anyone interested in sharing reports? Perhaps even as an anonymous format?

[ECO]

I'd be interested in seeing some reports from other people's runs. I'm always keen to compare our instrument's data output, even in a very summarised format such as this, with other instruments around the world. Is anyone interested in sharing reports? Perhaps even as an anonymous format?

That would be an excellent resource for group-troubleshooting. I'll download it and play with it myself and see if we can't whip up some sort of wiki-compilation of outputs.

edit: What would also be great is if this could be adapted to display multiple reports over time...so one can track performance and even compare directly against old runs.

[simonandrews]

I'd be really interested to see some more report from other sites. Apart from anything else I'd like to know whether the criteria I've set to call a test as a warn or fail are sensible on other people's data.

The idea of having some larger integrated reporting system for QC reports is tempting but I'm wary of stretching the original idea of FastQC too far. I kind of like the idea of connecting an install of the program to a reporting server so that the data from every report generated goes into a central system, but I'm not sure I'm going to find time to do that in the near future.

A quicker solution would be to have a site where you could upload the report zip files and make a browsable site where you could view these reports split by technology / chemistry / sample source etc. Would people be interested in this? More importantly would anyone be willing to put in some of their own data (anonymously of course)?

[NGSfan]

I think this is an interesting idea, although I think the novelty of comparing plots might wear off pretty soon. For example, people don't collect chromatograms from sanger sequencing any more

I agree, though, that it would be interesting to see things such as barcoded samples, extreme GC content, different machines, etc.