[med-svn] r12503 - trunk/packages/babraham/fastqc/trunk/debian

[Andreas Tille]

Author: tille
Date: 2012-11-07 13:25:44 +0000 (Wed, 07 Nov 2012)
New Revision: 12503

Modified:
   trunk/packages/babraham/fastqc/trunk/debian/README.Debian
   trunk/packages/babraham/fastqc/trunk/debian/docs
Log:
Write a more informative README.Debian in favour of installing the plain installation instructions from upstream


Modified: trunk/packages/babraham/fastqc/trunk/debian/README.Debian
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/README.Debian	2012-11-07 13:20:35 UTC (rev 12502)
+++ trunk/packages/babraham/fastqc/trunk/debian/README.Debian	2012-11-07 13:25:44 UTC (rev 12503)
@@ -1,6 +1,79 @@
 fastqc for Debian
 -----------------
 
-This package needs some testing and a man page.
+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.
 
- -- Steffen Moeller <moeller at debian.org>  Tue, 24 Apr 2012 20:05:34 +0200
+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
+<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 at debian.org>  Wed, 07 Nov 2012 14:24:25 +0100

Modified: trunk/packages/babraham/fastqc/trunk/debian/docs
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/docs	2012-11-07 13:20:35 UTC (rev 12502)
+++ trunk/packages/babraham/fastqc/trunk/debian/docs	2012-11-07 13:25:44 UTC (rev 12503)
@@ -1,4 +1,3 @@
-INSTALL.txt
 LICENSE.txt
 README.txt
 README.txt