Surprised no-one has mentioned HTMLDOC. For Ubuntu and similar simply:

sudo apt-get install htmldoc

then:

htmldoc --webpage -f output.pdf index.html

or just "htmldoc" for the GUI.

I just installed wkhtmltopdf and used it on your html file with this command:

wkhtmltopdf 20A.R2.QC.fq_fastqc/fastqc_report.html test.pdf

And I got a test.pdf file back with the correct contents. Here is the pdf file uploaded to imgur: http://imgur.com/f4fCz

Imgur converted the .pdf to .png so the quality is not great.

This is the script qcimg2pdf.sh) i use as part of Fastq workflow. I use some of the images from fastqc: Run it in the fastqc parent directories for different lanes....

#!/bin/bash
## qcimg2pdf.sh
echo "Usage: $0 -o output_prefix";

use ghostscript-9.02  ## if already exists in path comment this Line

if [[ $# -eq 0 || $# -gt 2 ]]
then
echo "No/wrong ($#) arguments detected "
echo "Run it where you have *fastqc directories";
exit 1 #exit shell script
fi

while getopts o: option
do
case $option in
o)
outprefix=$OPTARG
;;
esac
echo $outprefix;

if [[ $outprefix != "" ]];then
for j in `ls -d1 *fastqc` ;
 do
  echo $j ;

  convert \( -scale 500x500 $j/Images/per_base_quality.png $j/Images/per_base_gc_content.png +append \) \( -scale 500x500 $j/Images/per_sequence_quality.png $j/Images/per_sequence_gc_content.png +append \) -append -font Helvetica -pointsize 12 -gravity northeast -draw "translate +5,+5 text 80,80 '`grep -A5 Filename $j/fastqc_data.txt`'" QC.$j.pdf

 done

gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=qc-lanes.$outprefix.pdf QC.*.pdf

else
echo "use correct arguments with only -o "
exit 1 #exit shell script
fi

done

I would be interested in extracting the raw FastQC data as generic tables to render plots in R

If anyone would like to participate I could create a github repository for this "project".

Here is the XSLT stylesheet for FO:

the HTML document is not a valid XML document so I used xsltproc to fix the document before using FOP. Here is the Makefile:

all:fastqc.pdf

fastqc.fo:fastqc2fo.xsl fastqc_report.html
    xsltproc --html fastqc2fo.xsl fastqc_report.html > $@

fastqc.pdf:fastqc.fo
    fop  $< $@

The result was posted on slideshare: http://www.slideshare.net/lindenb/biostar17037

Edit: my output is missing one or two tables but you get the idea.

My company, Expected Behavior, has a service called DocRaptor that converts HTML to PDF or Excel format. Unlike wkhtmltopdf, DocRaptor generates fully functional PDF files, not just a PNG.

Here's a link to the home page:

http://docraptor.com/

And a link to the code example page. You make an HTTP POST request to DocRaptor's server, and we send your file back to you.

http://docraptor.com/examples

I just tried html to latex and after a few minutes I decided that you are right: must be an easier way.

@DK's approach seems the best.

http://htmltolatex.sourceforge.net/