Small things in docs
KVM doc
KVM BIOS setting
Minor doc fixes
Merge branch 'master' of github.com:pjotrp/cloudbiolinux

Conflicts:
	doc/linux_kvm.md
KVM OpenSuSE URL
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Flavor for neurodebian, a debian neuroscience package repository
It is just a flavor, not edition
Linuxbrew cannot be cloned since the base ubuntu 13.10 (from ubuntu cloud-images.ubuntu.com) does not have git installed
PyCharm broke indentation?
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Added preliminary listing from neurodebian packages, needs cleanup
Check for isolated input before printing shell exports. Fixes arq5x/gemini#308
Remove poorly specified transcripts the GTF file.

This removes transcripts without gene_id and transcript_id set;
it also removes transcripts which do not have a corresponding
FASTA sequence.
Add DEXseq GFF creation.
Remove GATK lite installation due to broken ftp and version getting dated. Fixes chapmanb/bcbio-nextgen-vm#9
Traverse genome directory locations properly.

This was breaking if you were running in a directory other than
the org_build dir.