add kraken to analysis and DB installation

merge with previous branch

merge qcsummary with last remote update
Merge pull request #507 from lpantano/upstream

kraken into QC-summary for rnaseq pipeline
Add R_package_path.

Some R packages like DEXSeq have scripts installed with the
packages. This helps us discover those scripts.
Add missing subprocess import.
Move unit test data to github hosted repo.

Made it a separate repository to limit the bcbio-nextgen
download size.

This hopefully will encourage more unit tests because anyone can
fork and add unit test data to the repository.
Pull from repository if bcbio-nextgen-test-data already exists.
Fix picard unit tests.

Fix bcbio-nextgen-test-data in .gitignore.
Add DEXseq counting.
Fail on combining counts if one of the input files is missing.
Add test for combing DEXseq count files into one file.
Use downsampled normal inputs next to samblaster discordant and split reads for delly structural variation detection to help improve run times. Refactor shared structural variant functionality into separate namespace
Proof of concept for new data-dictionary lookups.

The idea is that we can specify how the items are looked up in
the data dictionary in one place and have simple setters/getters
generated automatically.

This allows for much simpler testing because instead of having
to have a YAML file specified, you can create one with only the
attributes you need to set.

For example:
from bcbio.dd import dd
config = dd.set_gtf_file({}, 'foo') => {'genome_resources': {'rnaseq': {'transcripts': 'foo'}}}
gtf_file = dd.get_gtf_file(config) => 'foo'

It also allows easier integration with other tools using our wrappers since
they don't have to create our data dictionary.
Fix ChIP-Seq integration test.
Add optional checking functions to the data dictionary.
Provide Delly specific filtering on paired end and split read evidence. Prepare Delly specific exclude file
Move datadict lookups, set globals instead of using a class.

It is safe to do this with globals. locals has this warning in the
python docs:

'The contents of this dictionary should not be modified; changes
may not affect the values of local and free variables.'
globals does not have the same warning so it should be safe to modify
Add dexseq_gff, rRNA and the refFlat file to the genome resources.
Run dexseq from a bcbio-dict with unit test.
Fix for new downsample function signature.
Remove skip of dexseq unit test cleanup.