kraken into QC-summary for rnaseq pipeline

quite a big pull request, so please take a look if it makes sense. 

I just added to RNAseq pipeline, for now. Easy to add to the others, but maybe better to start with this. Add some metrics to the project-summary as well. % of detected reads in the kraken database, and link to the summary file.

I try to change the minimum as possible and reuse code. Some re-arrangement in QC-summary, so Rory, if you can look at it carefully, better. 

let me know if I miss something.

test for rnaseq is working, and when I run my particular test with `kraken : true` is working as well.

Right now need to set up `kraken_db` to use the database that the user has to have somewhere, but planning to add the database to be installed with bcbio soon. 

don't know if you want to wait until I change that as well, I thought that that was too many changes.

Probably I will do a pull request to cloudBioLinux to add kraken to be installed with the other tools as well.

sorry about that, I really don't know what happened. Fixing now, let you 
know tomorrow when is ready. thanks!

On 7/16/14, 20:23, Brad Chapman wrote:
>
> In bcbio/pipeline/qcsummary.py:
>
> >      qc_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"], "qc", data["description"]))
> >      metrics = {}
> > -    for program_name, qc_fn in to_run:
> > -        cur_qc_dir = os.path.join(qc_dir, program_name)
> > -        cur_metrics = qc_fn(bam_file, data, cur_qc_dir)
> > +    if has_aligned_reads(bam_file):
>
> This also has a merge issue, since we just checked in the |startswith| 
> fixes here. Could we skip the |has_aligned_reads| part and just run 
> QC. It's going to be extremely rare something has zero aligned reads 
> here and not sure it's going to blow anything up.
>
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> <https://github.com/chapmanb/bcbio-nextgen/pull/507/files#r15036158>.
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