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.

Configuration
-------------

Configuration files have been placed in /etc/fastqc/Configuration


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
<div> 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 <tille@debian.org>  Wed, 07 Nov 2012 14:24:25 +0100
