Sort the pairs output files before giving them back.

Some of the downstream tools expect paired FASTQ files to be
in order.
Make tophat look in rnaseq/tophat for the index files.

Also look for an index ending with _transcriptome.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Avoid update errors for existing installations with pre-existing install config YAMLs
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen