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 <[email protected]> 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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
