Readd samtools custom build used in gemini installation. Fixes arq5x/gemini#279
Correct flag value to install_brew() automated=True.

That's what I REALLY meant in 6375737108abc4de5a529685930f4de7c5a131bf.
Merge pull request #162 from glebkuznetsov/master

Correct flag value to install_brew() automated=True.
Do not fail on missing version information, instead re-install (chapmanb/bcbio-nextgen#405). Use custom version of delly exclusion file compatible with lumpy
Avoid estscan install which is problematic on Ubuntu 14.04. Fixes #163
Swap Pyrex to Pyrex-real.

Looks like the Pyrex pypi repository is dead and has moved to
Pyrex-real.
Remove gnuplot-py, it is missing from pypi at the moment.
fixed issues with libraries missing from pypi by adding --allow-unverified and --allow-external
wadded 'library(methods)' to fix broken R installer
Merge pull request #165 from timothyjlaurent/master

fixed issues with libraries missing from pypi by adding --allow-unverifi...
Update bcbio.variation v0.1.6
Add the ability to install nginx from a custom package
Provide a configuration file for the JWM desktop manager
Add a script for starting X
Add canFam3 to transcriptome preparation script.