sacCer2 to sacCer3
Move INDEX_FNs so outside packages can get a list of supported indexes.
updated yaml; sacCer2 => sacCer3
Remove automatic uploading to S3.
Merge pull request #169 from kern3020/master

updating sacCer2 to sacCer3
Include download of human ancestral sequence used by VEP LOFTEE plugin to assess loss of function mutations
Basic support for Arch linux detection: no package management but minimal detection to enable custom and other package installation. Fixes chapmanb/bcbio-nextgen#449
Turn on ancestral fasta human downloads by default
Ensure R library script creation happens inside temporary directory instead of bare file in current directory: chapmanb/bcbio-nextgen#453
Use GitHub mirror of RNA-SeQC jar to avoid Broad download issues with EC2: https://groups.google.com/d/msg/biovalidation/-mZBAYqLsZg/eqNGVa6wyH4J
Merge branch 'master' into nmdp-ngs-pipeline